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

Ecological divergence despite common mating sites: Genotypes and symbiotypes shed light on cryptic diversity in the black bean aphid species complex

Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.

Slow resistance evolution to neonicotinoids in field populations of wheat aphids revealed by insecticide resistance monitoring in China

BACKGROUND

The wheat aphids, Rhopalosiphum padi and Sitobion miscanthi, are serious agricultural insect pests of many crops. Neonicotinoid insecticides are commonly used as alternatives to organophosphate and pyrethroid insecticides for controlling wheat aphids.

RESULTS

Long-term monitoring of resistance to imidacloprid and acetamiprid in R. padi and S. miscanthi was carried out between 2007 and 2019. For this study, 344 specimens of the two wheat aphids were collected from field populations found in the main wheat production areas in China, from 2007 to 2019. In R. padi, the fluctuation in resistance was 14.7 times for imidacloprid and 1.4 times for acetamiprid; in S. miscanthi, it was 9.7 times for imidacloprid and 6.5 times for acetamiprid.

CONCLUSION

Our results demonstrated that both R. padi and S. miscanthi tended to have higher resistance to imidacloprid compared with acetamiprid. However, it is difficult for wheat aphids to develop a high level of neonicotinoid resistance given the pest control practices used in China. These results should be useful for the biorational application and resistance management of neonicotinoid insecticides. © 2021 Society of Chemical Industry.

The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates

Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (F_IS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.

Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia

Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, a new Phytophthora species was described in Colombia from tree tomato (Solanum betaceum), a semi-domesticated fruit grown in northern South America. Comprehensive phylogenetic, morphological, population genetic analyses, and infection assays to characterize this new species, were conducted. All data support the description of the new species, Phytophthora betacei sp. nov. Phylogenetic analyses suggest that this new species belongs to clade 1c of the genus Phytophthora and is a close relative of the potato late blight pathogen, P. infestans. Furthermore, it appeared as the sister group of the P. andina strains collected from wild Solanaceae (clonal lineage EC-2). Analyses of morphological and physiological characters as well as host specificity showed high support for the differentiation of these species. Based on these results, a complete description of the new species is provided and the species boundaries within Phytophthora clade 1c in northern South America are discussed.

Fundamental and realized feeding niche breadths of sexual and asexual stick insects

The factors contributing to the maintenance of sex over asexuality in natural populations remain unclear. Ecological divergences between sexual and asexual lineages could help to maintain reproductive polymorphisms, at least transiently, but the consequences of asexuality for the evolution of ecological niches are unknown. Here, we investigated how niche breadths change in transitions from sexual reproduction to asexuality. We used host plant ranges as a proxy to compare the realized feeding niche breadths of five independently derived asexual Timema stick insect species and their sexual relatives at both the species and population levels. Asexual species had systematically narrower realized niches than sexual species, though this pattern was not apparent at the population level. To investigate how the narrower realized niches of asexual species arise, we performed feeding experiments to estimate fundamental niche breadths but found no systematic differences between reproductive modes. The narrow realized niches found in asexual species are therefore probably a consequence of biotic interactions such as predation or competition, that constrain realized niche size in asexuals more strongly than in sexuals.

Daphnia females adjust sex allocation in response to current sex ratio and density

Cyclical parthenogenesis presents an interesting challenge for the study of sex allocation, as individuals' allocation decisions involve both the choice between sexual and asexual reproduction, and the choice between sons and daughters. Male production is therefore expected to depend on ecological and evolutionary drivers of overall investment in sex, and those influencing male reproductive value during sexual periods. We manipulated experimental populations, and made repeated observations of natural populations over their growing season, to disentangle effects of population density and the timing of sex from effects of adult sex ratio on sex allocation in cyclically parthenogenetic Daphnia magna. Male production increased with population density, the major ecological driver of sexual reproduction; however, this response was dampened when the population sex ratio was more male-biased. Thus, in line with sex ratio theory, we show that D. magna adjust offspring sex allocation in response to the current population sex ratio.

Aphid specialization on different summer hosts is associated with strong genetic differentiation and unequal symbiont communities despite a common mating habitat

Specialization on different host plants can promote evolutionary diversification of herbivorous insects. Work on pea aphids (Acyrthosiphon pisum) has contributed significantly to the understanding of this process, demonstrating that populations associated with different host plants exhibit performance trade-offs across hosts, show adaptive host choice and genetic differentiation and possess different communities of bacterial endosymbionts. Populations specialized on different secondary host plants during the parthenogenetic summer generations are also described for the black bean aphid (Aphis fabae complex) and are usually treated as different (morphologically cryptic) subspecies. In contrast to pea aphids, however, host choice and mate choice are decoupled in black bean aphids, because populations from different summer hosts return to the same primary host plant to mate and lay overwintering eggs. This could counteract evolutionary divergence, and it is currently unknown to what extent black bean aphids using different summer hosts are indeed differentiated. We addressed this question by microsatellite genotyping and endosymbiont screening of black bean aphids collected in summer from the goosefoot Chenopodium album (subspecies A. f. fabae) and from thistles of the genus Cirsium (subspecies A. f. cirsiiacanthoides) across numerous sites in Switzerland and France. Our results show clearly that aphids from Cirsium and Chenopodium exhibit strong and geographically consistent genetic differentiation and that they differ in their frequencies of infection with particular endosymbionts. The dependence on a joint winter host has thus not prevented the evolutionary divergence into summer host-adapted populations that appear to have evolved mechanisms of reproductive isolation within a common mating habitat.

The evolution of obligate sex: the roles of sexual selection and recombination

The evolution of sex is one of the greatest mysteries in evolutionary biology. An even greater mystery is the evolution of obligate sex, particularly when competing with facultative sex and not with complete asexuality. Here, we develop a stochastic simulation of an obligate allele invading a facultative population, where males are subject to sexual selection. We identify a range of parameters where sexual selection can contribute to the evolution of obligate sex: Especially when the cost of sex is low, mutation rate is high, and the facultative individuals do not reproduce sexually very often. The advantage of obligate sex becomes larger in the absence of recombination. Surprisingly, obligate sex can take over even when the population has a lower mean fitness as a result. We show that this is due to the high success of obligate males that can compensate the cost of sex.

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.

The distribution of sexual reproduction of the geographic parthenogen Eucypris virens (Crustacea: Ostracoda) matches environmental gradients in a temporary lake

Niche segregation may prevent competitive exclusion and promote local coexistence. This typically results in the occupation of different habitats. In the freshwater ostracod Eucypris virens (Jurine, 1820), the distribution of sexual and parthenogenetic populations in the temporary Lake Caracuel, central Spain, was not homogeneous. Parthenogens were found everywhere including the littoral, whereas sexuals were restricted to the centre. We investigated the hypothesis that spatial distribution responded to ecological differences. We studied the ecological significance of this segregation by linking environmental data to male presence, sexual fraction, ploidy, and genetic structure of our model organism in 12 ponds in the lake basin. Hydro-chemical and biological data indicated that the observed segregation is not only spatial but also ecological, with sexual E. virens occurring in ponds with shorter and probably more unpredictable hydroperiod. The correlations between environmental gradients and E. virens population structure suggest that sexual and parthenogenetic lineages are ecologically segregated. Sexual populations appeared restricted to sufficiently unpredictable environments, while parthenogens dominated environments with longer hydroperiods. Local coexistence seems mediated by spatial heterogeneity in habitat stability.

Modelling the geographical range of a species with variable life-history

We show how a climatic niche model can be used to describe the potential geographic distribution of a pest species with variable life-history, and illustrate how to estimate biogeographic pest threats that vary across space. The models were used to explore factors that affect pest risk (irrigation and presences of host plant). A combination of current distribution records and published experimental data were used to construct separate models for the asexual and sexual lineages of Rhopalosiphum padi (Linnaeus) (Hemiptera: Aphididae). The two models were combined with knowledge of host plant presence to classify the global pest risk posed by R. padi. Whilst R. padi has a relatively limited area in which sexual lineages can persist year round, a much larger area is suitable for transient sexual and asexual lineages to exist. The greatest risk of establishment of persistent sexual and asexual populations is in areas with warm temperate climates. At the global scale the models show very little difference in risk patterns between natural rainfall and irrigation scenarios, but in Australia, the amount of land suitable for persistent asexual and transient sexual populations decreases (by 20%) if drought stress is no longer alleviated by irrigation. This approach proved useful for modelling the potential distribution of a species that has a variable life-history. We were able to use the model outputs to examine factors such as irrigation practices and host plant presence that altered the nature (transient or permanent) and extent of pest risk. The composite niche maps indicate pest risk in terms that are useful to both biosecurity agencies and pest managers.

The effects of reproductive specialization on energy costs and fitness genetic variances in cyclical and obligate parthenogenetic aphids

Organisms with coexisting sexual and asexual populations are ideal models for studying the consequences of either reproductive mode on the quantitative genetic architecture of life-history traits. In the aphid Rhopalosiphum padi, lineages differing in their sex investment coexist but all share a common parthenogenetic phase. Here, we studied multiple genotypes of R. padi specialized either for sexual and asexual reproduction and compared their genetic variation in fitness during the parthenogenetic phase. Specifically, we estimated maintenance costs as standard metabolic rate (SMR), together with fitness (measured as the intrinsic rate of increase and the net reproductive rate). We found that genetic variation (in terms of broad-sense heritability) in fitness was higher in asexual genotypes compared with sexual genotypes. Also, we found that asexual genotypes exhibited several positive genetic correlations indicating that body mass, whole-animal SMR, and apterous individuals production are contributing to fitness. Hence, it appears that in asexual genotypes, energy is fully allocated to maximize the production of parthenogenetic individuals, the simplest possible form of aphid repertoire of life-histories strategies.

Climate effects on life cycle variation and population genetic architecture of the black bean aphid, Aphis fabae

Aphid species may exhibit different reproductive modes ranging from cyclical to obligate parthenogenesis. The distribution of life cycle variation in aphids is generally determined by ecological forces, mainly climate, because only sexually produced diapausing eggs can survive harsh winters or periods of absence of suitable host plants. Aphids are thus interesting models to investigate intrinsic and environmental factors shaping the competition among sexual and asexual lineages. We conducted a Europe-wide sampling of black bean aphids, Aphis fabae, and combined population genetic analyses based on microsatellite data with an experimental determination of life cycle strategies. Aphids were collected from broad beans (Vicia faba) as well as some Chenopodiaceae, but we detected no genetic differentiation between aphids from different host plants. Consistent with model predictions, life cycle variation was related to climate, with aphids from areas with cold winters investing more in sexual reproduction than aphids from areas with mild winters. Accordingly, only populations from mild areas exhibited a clear genetic signature of clonal reproduction. These differences arise despite substantial gene flow over large distances, which was evident from a very low geographic population structure and a lack of isolation-by-distance among 18 sites across distances of more than 1000 km. There was virtually no genetic differentiation between aphids with different reproductive modes, suggesting that new asexual lineages are formed continuously. Indeed, a surprising number of A. fabae genotypes even from colder climates produced some parthenogenetic offspring under simulated winter conditions. From this we predict that a shift to predominantly asexual reproduction could take place rapidly under climate warming.

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.

The invasion route for an insect pest species: the tobacco aphid in the New World

Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and/or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or 'superclones' in asexually reproducing organisms.

Allelic and genotypic diversity in long-term asexual populations of the pea aphid, Acyrthosiphon pisum in comparison with sexual populations

Many aphid species exhibit geographical variation in the mode of reproduction that ranges from cyclical parthenogenesis with a sexual phase to obligate parthenogenesis (asexual reproduction). Theoretical studies predict that organisms reproducing asexually should maintain higher allelic diversity per locus but lower genotypic diversity than organisms reproducing sexually. To corroborate this hypothesis, we evaluated genotypic and allelic diversities in the sexual and asexual populations of the pea aphid, Acyrthosiphon pisum (Harris). Microsatellite analysis revealed that populations in central Japan are asexual, whereas populations in northern Japan are obligatorily sexual. No mixed populations were detected in our study sites. Phylogenetic analysis using microsatellite data and mitochondrial cytochrome oxidase subunit I (COI) gene sequences revealed a long history of asexuality in central Japan and negated the possibility of the recent origin of the asexual populations from the sexual populations. Asexual populations exhibited much lower genotypic diversity but higher allelic richness per locus than did sexual populations. Asexual populations consisted of a few predominant clones that were considerably differentiated from one another. Sexual populations on alfalfa, an exotic plant in Japan, were most closely related to asexual populations associated with Vicia sativa L. The alfalfa-associated sexual populations harboured one COI haplotype that was included in the haplotype clade of the asexual populations. Available evidence suggests that the sexuality of the alfalfa-associated populations has recently been restored through the northward migration and colonization of alfalfa by V. sativa-associated lineages. Therefore, our results support the theoretical predictions and provide a new perspective on the origin of sexual populations.

Short-term population differences in the genetic architecture of life history traits related to sexuality in an aphid species

One of the most important factors that determine the evolutionary trajectory of a suite of traits in a population is the structure of the genetic variance-covariance matrix (G). We studied the cyclically parthenogenetic aphid Rhopalosiphum padi, whose populations exhibit two types of reproductive lineages respectively specialized in sexuality (that is, cyclically parthenogenetic lineages) and in asexuality (that is, obligate parthenogenetic lineages). We compared the quantitative genetics of life histories in these two lineage types. Our results suggest that both, the elements and the whole structure of the resulting G matrices differ in the very short term, between lineage types. This would involve the evolution toward different evolutionary optima in the same population, depending on whether sexual or asexual lineages predominate. Since sexual and asexual lineages vary seasonally in their abundance, a fluctuating selective regime has been proposed for this species, which would contribute to the maintenance of the reproductive polymorphism that these populations exhibit.