Using a meiosis detection toolkit to investigate ancient asexual "scandals" and the evolution of sex

Sexual reproduction is the dominant reproductive mode in eukaryotes but, in many taxa, it has never been observed. Molecular methods that detect evidence of sex are largely based on the genetic consequences of sexual reproduction. Here we describe a powerful new approach to directly search genomes for genes that function in meiosis. We describe a "meiosis detection toolkit", a set of meiotic genes that represent the best markers for the presence of meiosis. These genes are widely present in eukaryotes, function only in meiosis and can be isolated by degenerate PCR. The presence of most, or all, of these genes in a genome would suggest they have been maintained for meiosis and, implicitly, sexual reproduction. In contrast, their absence would be consistent with the loss of meiosis and asexuality. This approach will help to understand both meiotic gene evolution and the capacity for meiosis and sex in putative obligate asexuals.     

Male sterility in triploid dandelions: asexual females vs. asexual hermaphrodites

Male reproductive output, pollen in plants and sperm in animals has been shown to constitute a substantial cost for many organisms. In parthenogenetic hermaphrodites, selection is therefore expected to reduce the allocation of resources to male reproductive output. However, sustained production of pollen or sperm has been observed in numerous asexual hermaphrodites. We studied the widespread production of pollen by triploid asexual dandelions, Taraxacum sect. Ruderalia, comparing rare male sterile individuals with pollen producing asexuals. We found that individuals can show plasticity in the production of pollen, but that it is nevertheless possible to distinguish between (facultatively) male sterile asexuals and male fertile asexuals. Based on evidence from genetic markers and crosses, we conclude that the male sterility in asexual dandelions is caused by nuclear genes, in contrast to the cytoplasmically inherited male sterility previously found in sexual dandelions. Male sterile lineages did not produce more seeds per flower head, heavier seeds or seeds that were more viable. However, male sterile plants did produce more seed heads and hence more seeds than pollen producing ones, indicating that they were able to reallocate resources toward seed production. Considering the difference in seed production, it remains puzzling that not more asexual dandelions are male sterile.     

Sexual and asexual Taraxacum species

The genus Taraxacum is a widely dispersed, ecologically variable taxon of some 2000 sexual and apomictic (agarnospermous) species. Data from numerous studies are used to examine the influences sexuality and apomixis have had on its evolution, geographical distribution and ecological diversification. A new explanation is given of the geographical distribution of sexual and apomictic forms, and the role of polyploidy in buffering apomicts against the effects of an accumulation of deleterious mutations is examined.     

Diversification in sexual and asexual organisms

Abstract Sexual reproduction has long been proposed as a major factor explaining the existence of species and species diversity. Yet, the importance of sex for diversification remains obscure because of a lack of critical theory, difficulties of applying universal concepts of species and speciation, and above all the scarcity of empirical tests. Here, we use genealogical theory to compare the relative tendency of strictly sexual and asexual organisms to diversify into discrete genotypic and morphological clusters. We conclude that asexuals are expected to display discrete clusters similar to those found in sexual organisms. Whether sexuals or asexuals display stronger clustering depends on a number of factors, but in at least some scenarios asexuals should display a stronger pattern. Confounding factors aside, the only explanation we identify for stronger patterns of diversification in sexuals than asexuals is if the faster rates of adaptive change conferred by sexual reproduction promote greater clustering. Quantitative comparisons of diversification in related sexual and asexual taxa are needed to resolve this issue. The answer should shed light not only on the importance of the different stages leading to diversification, but also on the adaptive consequences of sex, still largely unexplored from a macroevolutionary perspective.     

Genomic signatures of ancient asexual lineages

Ancient asexuals – organisms that have lived without sex for millions of years – offer unique opportunities for discriminating among the various theories of the maintenance of sex. The last few years have seen molecular studies of a number of putative ancient asexual lineages, including bdelloid rotifers, Darwinulid ostracods, and mycorrhizal fungi. To help make sense of the diverse findings of such studies, we present a review and classification of the predicted effects of loss of sex on the eukaryotic genome. These include: (1) direct effects on the genetic structure of individuals and populations; (2) direct effects on the mutation rate due to the loss of the sexual phase; (3) decay of genes specific to sex and recombination; (4) effects of the cessation of sexual selection; (5) dis-adaptation due to the reduced efficiency of selection; and (6) adaptations to asexuality. We discuss the utility of the various predictions for detecting ancient asexuality, for testing hypotheses of the reversibility of a transition to asexuality, and for discriminating between theories of sex. In addition, we review the current status of putative ancient asexuals.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society 2003, 79 , 69–84.     

Limits to adaptation in asexual populations

In asexual populations, the rate of adaptation is basically limited by the frequency and properties of spontaneous beneficial mutations. Hence, knowledge of these mutational properties and how they are affected by particular evolutionary conditions is a precondition for understanding the process of adaptation. Here, we address how the rate of adaptation of asexual populations is limited by its population size and mutation rate, as well as by two factors affecting the fraction of mutations that confer a benefit, i.e. the initial adaptedness of the population and the variability of the environment. These factors both influence which mutations are likely to occur, as well as the probability that they will ultimately contribute to adaptation. We attempt to separate the consequences of these basic population features in terms of their effect on the rate of adaptation by using results from evolution experiments with microorganisms.     

Transposon proliferation in an asexual parasitoid

The widespread occurrence of sex is one of the most elusive problems in evolutionary biology. Theory predicts that asexual lineages can be driven to extinction by uncontrolled proliferation of vertically transmitted transposable elements (TEs), which accumulate because of the inefficiency of purifying selection in the absence of sex and recombination. To test this prediction, we compared genome-wide TE load between a sexual lineage of the parasitoid wasp Leptopilina clavipes and a lineage of the same species that is rendered asexual by Wolbachia-induced parthenogenesis. We obtained draft genome sequences at 15-20× coverage of both the sexual and the asexual lineages using next-generation sequencing. We identified transposons of most major classes in both lineages. Quantification of TE abundance using coverage depth showed that copy numbers in the asexual lineage exceeded those in the sexual lineage for DNA transposons, but not LTR and LINE-like elements. However, one or a small number of gypsy-like LTR elements exhibited a fourfold higher coverage in the asexual lineage. Quantitative PCR showed that high loads of this gypsy-like TE were characteristic for 11 genetically distinct asexual wasp lineages when compared to sexual lineages. We found no evidence for an overall increase in copy number for all TE types in asexuals as predicted by theory. Instead, we suggest that the expansions of specific TEs are best explained as side effects of (epi)genetic manipulations of the host genome by Wolbachia. Asexuality is achieved in a myriad of ways in nature, many of which could similarly result in TE proliferation.     

Emergent neutrality in adaptive asexual evolution

In nonrecombining genomes, genetic linkage can be an important evolutionary force. Linkage generates interference interactions, by which simultaneously occurring mutations affect each other's chance of fixation. Here, we develop a comprehensive model of adaptive evolution in linked genomes, which integrates interference interactions between multiple beneficial and deleterious mutations into a unified framework. By an approximate analytical solution, we predict the fixation rates of these mutations, as well as the probabilities of beneficial and deleterious alleles at fixed genomic sites. We find that interference interactions generate a regime of emergent neutrality: all genomic sites with selection coefficients smaller in magnitude than a characteristic threshold have nearly random fixed alleles, and both beneficial and deleterious mutations at these sites have nearly neutral fixation rates. We show that this dynamic limits not only the speed of adaptation, but also a population's degree of adaptation in its current environment. We apply the model to different scenarios: stationary adaptation in a time-dependent environment and approach to equilibrium in a fixed environment. In both cases, the analytical predictions are in good agreement with numerical simulations. Our results suggest that interference can severely compromise biological functions in an adapting population, which sets viability limits on adaptive evolution under linkage.     

Environmental adaptation in an asexual invasive insect

Parthenogenetic reproduction is generally associated with low genetic variance and therefore reduced ability for environmental adaptation, and this could limit the potential invasiveness of introduced species that reproduce asexually. However, the hemlock woolly adelgid is an asexual invasive insect that has spread across a large geographic temperature gradient in its introduced range. Consequently, this insect has shown significant variation in cold hardiness among populations. We hypothesized that the increased cold hardiness of northern populations represents an adaptation to the colder temperatures. To test this, we collected individual adelgid from populations spanning their invaded range and inoculated them into a common thermal environment. We then experimentally sampled the supercooling point of the progeny of these adelgids and compared these results with tests of the supercooling point of adelgid sampled directly from their source populations. The results showed that the same significant differences in supercooling that was found among geographically distinct populations existed even when the adelgid was reared in a common environment, indicating a genetic basis for the variation in cold hardiness. These findings support the hypothesis that the adelgid has adapted to the colder environment as it has expanded its distribution in its invaded range.     

Liberation of asexual propagules in the Mucorales

The liberation of asexual propagules in the Mucorales was investigated by means of wind-tunnel experiments. Some species do not liberate propagules into an air stream, others liberate single spores or groups of spores. The effect of the relative humidity of the air stream upon propagule liberation has also been considered.     

Neurospora crassa ve-1 affects asexual conidiation

The velvet factor of the homothallic fungus Aspergillus nidulans promotes sexual fruiting body formation. The encoding veA gene is conserved among fungi, including the ascomycete Neurospora crassa. There, the orthologous ve-1 gene encodes a deduced protein with high similarity to A. nidulans VeA. Cross-complementation experiments suggest that both the promoter and the coding sequence of N. crassa ve-1 are functional to complement the phenotype of an A. nidulans deletion mutant. Moreover, ve-1 expression in the heterologous host A. nidulans results in development of reproductive structures in a light-dependent manner, promoting sexual development in the darkness while stimulating asexual sporulation under illumination. Deletion of the N. crassa ve-1 locus by homologous gene replacement causes formation of shortened aerial hyphae accompanied by a significant increase in asexual conidiation, which is not light-dependent. Our data suggest that the conserved velvet proteins of A. nidulans and N. crassa exhibit both similar and different functions to influence development of these two ascomycetes.     

Constraints on the evolution of asexual reproduction

Sexual reproduction is almost ubiquitous among multicellular organisms even though it entails severe fitness costs. To resolve this apparent paradox, an extensive body of research has been devoted to identifying the selective advantages of recombination that counteract these costs. Yet, how easy is it to make the transition to asexual reproduction once sexual reproduction has been established for a long time? The present review approaches this question by considering factors that impede the evolution of parthenogenesis in animals. Most importantly, eggs need a diploid chromosome set in most species in order to develop normally. Next, eggs may need to be activated by sperm, and sperm may also contribute centrioles and other paternal factors to the zygote. Depending on how diploidy is achieved mechanistically, further problems may arise in offspring that stem from 'inbreeding depression' or inappropriate sex determination systems. Finally, genomic imprinting is another well-known barrier to the evolution of asexuality in mammals. Studies on species with occasional, deficient parthenogenesis indicate that the relative importance of these constraints may vary widely. The intimate evolutionary relations between haplodiploidy and parthenogenesis as well as implications for the clade selection hypothesis of the maintenance of sexual reproduction are also discussed.     

Symbiosis between grasses and asexual fungal endophytes

The symbiosis between vertically transmitted asexual endophytic fungi and grasses is common and generally considered to be mutualistic. Recent studies have accumulated evidence of negative effects of endophytes on plant fitness, prompting a debate on the true nature of the symbiosis. Genetic factors in each of the two partners show high variability and have a range of effects (from positive to negative) on plant fitness. In addition, interacting environmental factors might modify the nature of the symbiosis. Finally, competition and multitrophic interactions among grass consumers are influenced by endophytes, and the effects of plant neighbours or consumers could feedback to affect plant fitness. We propose a mutualism-parasitism continuum for the symbiosis between asexual endophytes and grasses, which is similar to the associations between plants and mycorrhizal fungi.