Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene

BACKGROUND

DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD).

RESULTS

We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory.

CONCLUSIONS

Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover approximately 200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach.

Mutation and the evolution of recombination

Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.

Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli

Knowledge of the mutational parameters that affect the evolution of organisms is of key importance in understanding the evolution of several characteristics of many natural populations, including recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous mutations that affect fitness in a mutator strain of Escherichia coli and review some of the estimation methods associated with mutation accumulation (MA) experiments. We performed an MA experiment where we followed the evolution of 50 independent mutator lines that were subjected to repeated bottlenecks of a single individual for approximately 1150 generations. From the decline in mean fitness and the increase in variance between lines, we estimated a minimum mutation rate to deleterious mutations of 0.005 (+/-0.001 with 95% confidence) and a maximum mean fitness effect per deleterious mutation of 0.03 (+/-0.01 with 95% confidence). We also show that any beneficial mutations that occur during the MA experiment have a small effect on the estimate of the rate and effect of deleterious mutations, unless their rate is extremely large. Extrapolating our results to the wild-type mutation rate, we find that our estimate of the mutational effects is slightly larger and the inferred deleterious mutation rate slightly lower than previous estimates obtained for non-mutator E. coli.

The role of advantageous mutations in enhancing the evolution of a recombination modifier

Although the evolution of recombination is still a major problem in evolutionary genetics, recent theoretical studies have shown that recombination can evolve by breaking down interference ("Hill-Robertson effects") among multiple loci. This leads to selection on a recombination modifier in a population subject to recurrent deleterious mutation. Here, we use computer simulations to investigate the evolution of a recombination modifier under three different scenarios of recurrent mutation in a finite population: (1) mutations are deleterious only, (2) mutations are advantageous only, and (3) there is a mixture of deleterious and advantageous mutations. We also investigate how linkage disequilibrium, the strength of selection acting on a modifier, and effective population size change under the different scenarios. We observe that adding even a small number of advantageous mutations increases the fixation rate of modifiers that increase recombination, especially if the effects of deleterious mutations are weak. However, the strength of selection on a modifier is less than the summed strengths had there been deleterious mutations only and advantageous mutations only.

Fungal sex and pathogenesis

Human fungal pathogens are associated with diseases ranging from dandruff and skin colonization to invasive bloodstream infections. The major human pathogens belong to the Candida, Aspergillus, and Cryptococcus clades, and infections have high and increasing morbidity and mortality. Many human fungal pathogens were originally assumed to be asexual. However, recent advances in genome sequencing, which revealed that many species have retained the genes required for the sexual machinery, have dramatically influenced our understanding of the biology of these organisms. Predictions of a rare or cryptic sexual cycle have been supported experimentally for some species. Here, I examine the evidence that human pathogens reproduce sexually. The evolution of the mating-type locus in ascomycetes (including Candida and Aspergillus species) and basidiomycetes (Malassezia and Cryptococcus) is discussed. I provide an overview of how sex is suppressed in different species and discuss the potential associations with pathogenesis.

Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns

We have compared the transcriptomic profiles of microdissected live ovules at four developmental stages between a diploid sexual and diploid apomictic Boechera. We sequenced >2 million SuperSAGE tags and identified (1) heterochronic tags (n = 595) that demonstrated significantly different patterns of expression between sexual and apomictic ovules across all developmental stages, (2) stage-specific tags (n = 577) that were found in a single developmental stage and differentially expressed between the sexual and apomictic ovules, and (3) sex-specific (n = 237) and apomixis-specific (n = 1106) tags that were found in all four developmental stages but in only one reproductive mode. Most heterochronic and stage-specific tags were significantly downregulated during early apomictic ovule development, and 110 were associated with reproduction. By contrast, most late stage-specific tags were upregulated in the apomictic ovules, likely the result of increased gene copy number in apomictic (hexaploid) versus sexual (triploid) endosperm or of parthenogenesis. Finally, we show that apomixis-specific gene expression is characterized by a significant overrepresentation of transcription factor activity. We hypothesize that apomeiosis is associated with global downregulation at the megaspore mother cell stage. As the diploid apomict analyzed here is an ancient hybrid, these data are consistent with the postulated link between hybridization and asexuality and provide a hypothesis for multiple evolutionary origins of apomixis in the genus Boechera.

[Sexuality and pathogenicity in Aspergillus fumigatus: is there any relationship?]

BACKGROUND

Aspergillus fumigatus, like many other fungal species of clinical relevance, has been traditionally regarded as an asexual organism. However, in last few years several pieces of evidence question this such assumption, suggesting that the sexual state of A. fumigatus may still be undiscovered. These investigations have finally led to the recent discovery of a teleomorph stage of A. fumigatus, which has been named Neosartorya fumigata.

AIMS

To review the most important findings on A. fumigatus sexuality and discuss the possible implications of such findings on its pathogenicity.

METHODS

A bibliographic search was performed to find the main works that study the sexuality of fungal pathogens and, especially, of A. fumigatus. Moreover, data from our recent investigations in this field were also introduced to the discussion.

RESULTS

The existence of a teleomorph for A. fumigatus could have significant clinical repercussions, as sexual reproduction might produce offspring with increased virulence and/or resistance to antifungal agents. In this sense, the results of our investigations suggest the existence of an association between the MAT1-1 mating type and the invasiveness of A. fumigatus isolates.

CONCLUSIONS

The study of the sexual reproduction of the fungal pathogens and its possible relationship with virulence will continue to be a topic of interest during the next years, not only because of its basic interest, but also for the possible clinical repercussions.

Multi-site adaptation in the presence of infrequent recombination

The adverse effect of co-inheritance linkage of a large number of sites on adaptation has been studied extensively for asexual populations. However, it is insufficiently understood for multi-site populations in the presence of recombination. In the present work, motivated by our studies of HIV evolution in infected patients, we consider a model of haploid populations with infrequent recombination. We assume that small quantities of beneficial alleles preexist at a large number of sites and neglect new mutation. Using a generalized form of the traveling wave method, we show that the effectiveness of recombination is impeded and the adaptation rate is decreased by inter-sequence correlations, arising due to the fact that some pairs of homologous sites have common ancestors existing after the onset of adaptation. As the recombination rate per individual becomes smaller, site pairs with common ancestors become more frequent, making recombination even less effective. In addition, an increasing number of sites become identical by descent across large samples of sequences, causing reversion of the direction of evolution and the loss of beneficial alleles at these sites. As a result, within a 10-fold range of the recombination rate, the average adaptation rate falls from 90% of the infinite-recombination value down to 10%. The entire transition from almost maximum to almost zero may occur at very small recombination rates. Interestingly, the strong effect of linkage on the adaptation rate is predicted in the absence of average linkage disequilibrium (Lewontin's measure).

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks1-3, to what extent genetic epistasis reflects biologically meaningful interactions remains unclear4-6. We address this question by in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of E. coli and S. cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant, and surprisingly, often occurs between reactions without overlapping functions. We offered mechanistic explanations of these findings and experimentally validated them for 61 S. cerevisiae gene pairs.

Deleterious mutations and selection for sex in finite diploid populations

In diploid populations, indirect benefits of sex may stem from segregation and recombination. Although it has been recognized that finite population size is an important component of selection for recombination, its effects on selection for segregation have been somewhat less studied. In this article, we develop analytical two- and three-locus models to study the effect of recurrent deleterious mutations on a modifier gene increasing sex, in a finite diploid population. The model also incorporates effects of mitotic recombination, causing loss of heterozygosity (LOH). Predictions are tested using multilocus simulations representing deleterious mutations occurring at a large number of loci. The model and simulations show that excess of heterozygosity generated by finite population size is an important component of selection for sex, favoring segregation when deleterious alleles are nearly additive to dominant. Furthermore, sex tends to break correlations in homozygosity among selected loci, which disfavors sex when deleterious alleles are either recessive or dominant. As a result, we find that it is difficult to maintain costly sex when deleterious alleles are recessive. LOH tends to favor sex when deleterious mutations are recessive, but the effect is relatively weak for rates of LOH corresponding to current estimates (of the order 10(-4)-10(-5)).

Sex, mixability, and modularity

The assumption that different genetic elements can make separate contributions to the same quantitative trait was originally made in order to reconcile biometry and Mendelism and ever since has been used in population genetics, specifically for the trait of fitness. Here we show that sex is responsible for the existence of separate genetic effects on fitness and, more generally, for the existence of a hierarchy of genetic evolutionary modules. Using the tools developed in the process, we also demonstrate that in terms of their fitness effects, separation and fusion of genes are associated with the increase and decrease of the recombination rate between them, respectively. Implications for sex and evolution theory are discussed.

Heterothallism in Saccharomyces cerevisiae isolates from nature: effect of HO locus on the mode of reproduction

Understanding the evolution of sex and recombination, key factors in the evolution of life, is a major challenge in biology. Studies of reproduction strategies of natural populations are important to complement the theoretical and experimental models. Fungi with both sexual and asexual life cycles are an interesting system for understanding the evolution of sex. In a study of natural populations of yeast Saccharomyces cerevisiae, we found that the isolates are heterothallic, meaning their mating type is stable, while the general belief is that natural S. cerevisiae strains are homothallic (can undergo mating-type switching). Mating-type switching is a gene-conversion process initiated by a site-specific endonuclease HO; this process can be followed by mother-daughter mating. Heterothallic yeast can mate with unrelated haploids (amphimixis), or undergo mating between spores from the same tetrad (intratetrad mating, or automixis), but cannot undergo mother-daughter mating as homothallic yeasts can. Sequence analysis of HO gene in a panel of natural S. cerevisiae isolates revealed multiple mutations. Good correspondence was found in the comparison of population structure characterized using 19 microsatellite markers spread over eight chromosomes and the HO sequence. Experiments that tested whether the mating-type switching pathway upstream and downstream of HO is functional, together with the detected HO mutations, strongly suggest that loss of function of HO is the cause of heterothallism. Furthermore, our results support the hypothesis that clonal reproduction and intratetrad mating may predominate in natural yeast populations, while mother-daughter mating might not be as significant as was considered.

Rate of adaptation in large sexual populations

Adaptation often involves the acquisition of a large number of genomic changes that arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise in different individuals and be combined later. In large populations, when the product of the population size N and the total beneficial mutation rate U(b) is large, many new beneficial alleles can be segregating in the population simultaneously. We calculate the rate of adaptation, v, in several models of such sexual populations and show that v is linear in NU(b) only in sufficiently small populations. In large populations, v increases much more slowly as log NU(b). The prefactor of this logarithm, however, increases as the square of the recombination rate. This acceleration of adaptation by recombination implies a strong evolutionary advantage of sex.

Sexual selection and animal personality

Consistent individual behavioural tendencies, termed "personalities", have been identified in a wide range of animals. Functional explanations for personality have been proposed, but as yet, very little consideration has been given to a possible role for sexual selection in maintaining differences in personality and its stability within individuals. We provide an overview of the available literature on the role of personality traits in intrasexual competition and mate choice in both human and non-human animals and integrate this into a framework for considering how sexual selection can generate and maintain personality. For this, we consider the evolution and maintenance of both main aspects of animal personality: inter-individual variation and intra-individual consistency.

Characterization of meiotic crossovers and gene conversion by whole-genome sequencing in Saccharomyces cerevisiae

BACKGROUND

Meiotic recombination alters frequency and distribution of genetic variation, impacting genetics and evolution. In the budding yeast, DNA double strand breaks (DSBs) and D loops form either crossovers (COs) or non-crossovers (NCOs), which occur at many sites in the genome. Differences at the nucleotide level associated with COs and NCOs enable us to detect these recombination events and their distributions.

RESULTS

We used high throughput sequencing to uncover over 46 thousand single nucleotide polymorphisms (SNPs) between two budding yeast strains and investigated meiotic recombinational events. We provided a detailed analysis of CO and NCO events, including number, size range, and distribution on chromosomes. We have detected 91 COs, very close to the average number from previous genetic studies, as well as 21 NCO events and mapped the positions of these events with high resolution. We have obtained DNA sequence-level evidence for a wide range of sizes of chromosomal regions involved in CO and NCO events. We show that a large fraction of the COs are accompanied by gene conversion (GC), indicating that meiotic recombination changes allelic frequencies, in addition to redistributing existing genetic variations.

CONCLUSION

This work is the first reported study of meiotic recombination using high throughput sequencing technologies. Our results show that high-throughput sequencing is a sensitive method to uncover at single-base resolution details of CO and NCO events, including some complex patterns, providing new clues about the mechanism of this fundamental process.

Effects of recombination on complex regulatory circuits

Mutation and recombination are the two main forces generating genetic variation. Most of this variation may be deleterious. Because recombination can reorganize entire genes and genetic circuits, it may have much greater consequences than point mutations. We here explore the effects of recombination on models of transcriptional regulation circuits that play important roles in embryonic development. We show that recombination has weaker deleterious effects on the expression phenotypes of these circuits than mutations. In addition, if a population of such circuits evolves under the influence of mutation and recombination, we find that three key properties emerge: (1) deleterious effects of mutations are reduced dramatically; (2) the diversity of genotypes in the population is greatly increased, a feature that may be important for phenotypic innovation; and (3) cis-regulatory complexes appear. These are combinations of regulatory interactions that influence the expression of one gene and that mitigate deleterious recombination effects.

Two-parameter characterization of chromosome-scale recombination rate

The genome-wide recombination rate (RR) of a species is often described by one parameter, the ratio between total genetic map length (G) and physical map length (P), measured in centimorgans per megabase (cM/Mb). The value of this parameter varies greatly between species, but the cause for these differences is not entirely clear. A constraining factor of overall RR in a species, which may cause increased RR for smaller chromosomes, is the requirement of at least one chiasma per chromosome (or chromosome arm) per meiosis. In the present study, we quantify the relative excess of recombination events on smaller chromosomes by a linear regression model, which relates the genetic length of chromosomes to their physical length. We find for several species that the two-parameter regression, G = G(0) + k x P , provides a better characterization of the relationship between genetic and physical map length than the one-parameter regression that runs through the origin. A nonzero intercept (G(0)) indicates a relative excess of recombination on smaller chromosomes in a genome. Given G(0), the parameter k predicts the increase of genetic map length over the increase of physical map length. The observed values of G(0) have a similar magnitude for diverse species, whereas k varies by two orders of magnitude. The implications of this strategy for the genetic maps of human, mouse, rat, chicken, honeybee, worm, and yeast are discussed.

Thelytokous parthenogenesis in the fungus-gardening ant Mycocepurus smithii (Hymenoptera: Formicidae)

The general prevalence of sexual reproduction over asexual reproduction among organisms testifies to the evolutionary benefits of recombination, such as accelerated adaptation to changing environments and elimination of deleterious mutations. Documented instances of asexual reproduction in groups otherwise dominated by sexual reproduction challenge evolutionary biologists to understand the special circumstances that might confer an advantage to asexual reproductive strategies. Here we report one such instance of asexual reproduction in the ants. We present evidence for obligate thelytoky in the asexual fungus-gardening ant, Mycocepurus smithii, in which queens produce female offspring from unfertilized eggs, workers are sterile, and males appear to be completely absent. Obligate thelytoky is implicated by reproductive physiology of queens, lack of males, absence of mating behavior, and natural history observations. An obligate thelytoky hypothesis is further supported by the absence of evidence indicating sexual reproduction or genetic recombination across the species' extensive distribution range (Mexico-Argentina). Potential conflicting evidence for sexual reproduction in this species derives from three Mycocepurus males reported in the literature, previously regarded as possible males of M. smithii. However, we show here that these specimens represent males of the congeneric species M. obsoletus, and not males of M. smithii. Mycocepurus smithii is unique among ants and among eusocial Hymenoptera, in that males seem to be completely absent and only queens (and not workers) produce diploid offspring via thelytoky. Because colonies consisting only of females can be propagated consecutively in the laboratory, M. smithii could be an adequate study organism a) to test hypotheses of the population-genetic advantages and disadvantages of asexual reproduction in a social organism and b) inform kin conflict theory.

For a Portuguese translation of the abstract, please see Abstract S1.

Red Queen dynamics with non-standard fitness interactions

Antagonistic coevolution between hosts and parasites can involve rapid fluctuations of genotype frequencies that are known as Red Queen dynamics. Under such dynamics, recombination in the hosts may be advantageous because genetic shuffling can quickly produce disproportionately fit offspring (the Red Queen hypothesis). Previous models investigating these dynamics have assumed rather simple models of genetic interactions between hosts and parasites. Here, we assess the robustness of earlier theoretical predictions about the Red Queen with respect to the underlying host-parasite interactions. To this end, we created large numbers of random interaction matrices, analysed the resulting dynamics through simulation, and ascertained whether recombination was favoured or disfavoured. We observed Red Queen dynamics in many of our simulations provided the interaction matrices exhibited sufficient ‘antagonicity’. In agreement with previous studies, strong selection on either hosts or parasites favours selection for increased recombination. However, fast changes in the sign of linkage disequilibrium or epistasis were only infrequently observed and do not appear to be a necessary condition for the Red Queen hypothesis to work. Indeed, recombination was often favoured even though the linkage disequilibrium remained of constant sign throughout the simulations. We conclude that Red Queen-type dynamics involving persistent fluctuations in host and parasite genotype frequencies appear to not be an artefact of specific assumptions about host-parasite fitness interactions, but emerge readily with the general interactions studied here. Our results also indicate that although recombination is often favoured, some of the factors previously thought to be important in this process such as linkage disequilibrium fluctuations need to be reassessed when fitness interactions between hosts and parasites are complex.

The Red Queen has become an eponym for rapid and perpetual evolutionary arms races between hosts and parasites. The Red Queen also lends her name to the idea that such arms races are at the core of the question of why sexual reproduction is so widespread among higher-level organisms. According to this view, recombination provides the hosts with an advantage that allows faster adaptation to the parasite population. To date, mathematical models trying to quantify Red Queen dynamics and the Red Queen hypothesis for the evolution of sex have generally made several simplifying assumptions about how host and parasite genotypes interact with each other (i.e., how they influence each other's fitness). In this article we present a model that allows for arbitrary patterns of fitness interactions between both parties. We demonstrate that the degree of ‘antagonicity’ in these interactions is decisive for whether Red Queen dynamics are observed, and assess the robustness of various previous results concerning the Red Queen hypothesis with respect to fitness interactions. Our results also make clear how difficult predictions of coevolutionary dynamics and selection for recombination are likely to be in real host-parasite systems.

Climate and agricultural context shape reproductive mode variation in an aphid crop pest

In aphids, reproductive mode is generally assumed to be selected for by winter climate. Sexual lineages produce frost-resistant eggs, conferring an advantage in regions with cold winters, while asexual lineages predominate in regions with mild winters. However, habitat and resource heterogeneities are known to exert a strong influence on sex maintenance and might modulate the effect of climate on aphid reproductive strategies. We carried out a hierarchical sampling in northern France to investigate whether reproductive mode variation of the aphid Rhopalosiphum padi is driven by winter climate conditions, by habitat and resource heterogeneities represented by a range of host plants or by both factors. We confirmed the coexistence in R. padi populations of two genetic clusters associated with distinct reproductive strategies. Asexual lineages predominated, whatever the surveyed year and location. However, we detected a between-year variation in the local contribution of both clusters, presumably associated with preceding winter severity. No evidence for host-driven niche differentiation was found in the field on six Poaceae among sexual and asexual lineages. Two dominant multilocus genotypes ( approximately 70% of the sample), having persisted over a 10-year period, were equally abundant on different plant species and locations, indicating their large ecological tolerance. Our results fit theoretical predictions of the influence of winter climate on the balance between sexual and asexual lineages. They also highlight the importance of current agricultural practices which seem to favour a small number of asexual generalist genotypes and their migration across large areas of monotonous environments.

The kin structure of sexual interactions

The origin of sexual reproduction involved the evolution of zygotes from separate genomes and, like other social processes, should therefore be amenable to analysis using kin selection theory. I consider how kin structure affects sexual interactions in three contexts--the evolution of sexual reproduction, sex allocation and sexual conflict. Kin structure helps explain the even-handed replication of paternal and maternal genes under outbreeding. Under inbreeding, it predicts altruistic failure to replicate by one half of the diploid genome. Kin structure predicts optimal sex ratios and potential conflicts over sex ratio within social groups and individuals. Sexual conflict predictably occurs as a function of (i) the probability that current sexual partners will reproduce together in future and (ii) between-partner relatedness. I conclude that systematically analysing the kin structure of sexual interactions helps illuminate their evolution.

No sex in fungus-farming ants or their crops

Asexual reproduction imposes evolutionary handicaps on asexual species, rendering them prone to extinction, because asexual reproduction generates novel genotypes and purges deleterious mutations at lower rates than sexual reproduction. Here, we report the first case of complete asexuality in ants, the fungus-growing ant Mycocepurus smithii, where queens reproduce asexually but workers are sterile, which is doubly enigmatic because the clonal colonies of M. smithii also depend on clonal fungi for food. Degenerate female mating anatomy, extensive field and laboratory surveys, and DNA fingerprinting implicate complete asexuality in this widespread ant species. Maternally inherited bacteria (e.g. Wolbachia, Cardinium) and the fungal cultivars can be ruled out as agents inducing asexuality. M. smithii societies of clonal females provide a unique system to test theories of parent-offspring conflict and reproductive policing in social insects. Asexuality of both ant farmer and fungal crop challenges traditional views proposing that sexual farmer ants outpace coevolving sexual crop pathogens, and thus compensate for vulnerabilities of their asexual crops. Either the double asexuality of both farmer and crop may permit the host to fully exploit advantages of asexuality for unknown reasons or frequent switching between crops (symbiont reassociation) generates novel ant-fungus combinations, which may compensate for any evolutionary handicaps of asexuality in M. smithii.

Inbreeding depression varies with investment in sex in a facultative parthenogen

The reproductive mode of facultative parthenogens allows recessive mutations that accumulate during the asexual phase to be unmasked following sexual reproduction. Longer periods of asexual reproduction should increase the accumulation of deleterious mutations within individuals, reduce population-level genetic diversity via competition and increase the probability of mating among close relatives. Having documented that the investment in sexual reproduction differs among populations and clones of Daphnia pulicaria, we ask if this variation is predictive of the level of inbreeding depression across populations. In four lake populations that vary in sex investment, we raised multiple families (mother, field-produced daughter, laboratory-produced daughter) on high food and estimated the fitness reduction in both sexually produced offspring relative to the maternal genotype. Inbred individuals had lower fitness than their field-produced siblings. The magnitude of fitness reduction in inbred offspring increased as population-level investment in sex decreased. However, there was less of a fitness reduction following sex in the field-produced daughters, suggesting that many field-collected mothers were involved in outcross mating.

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens

Theory predicts that partially asexual organisms may make the "best of both worlds": for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000-600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

Tests of sex allocation theory in simultaneously hermaphroditic animals

Sex allocation is a crucial life-history parameter in all sexual organisms. Over the last decades a body of evolutionary theory, sex allocation theory, was developed, which has yielded capital insight into the evolution of optimal sex allocation patterns and adaptive evolution in general. Most empirical work, however, has focused on species with separate sexes. Here I review sex allocation theory for simultaneous hermaphrodites and summarize over 50 empirical studies, which have aimed at evaluating this theory in a diversity of simultaneous hermaphrodites spanning nine animal phyla. These studies have yielded considerable qualitative support for several predictions of sex allocation theory, such as a female-biased sex allocation when the number of mates is limited, and a shift toward a more male-biased sex allocation with increasing numbers of mates. In contrast, many fundamental assumptions, such as the trade-off between male and female allocation, and numerous predictions, such as brooding limiting the returns from female allocation, are still poorly supported. Measuring sex allocation in simultaneously hermaphroditic animals remains experimentally demanding, which renders evaluation of more quantitative predictions a challenging task. I identify the main questions that need to be addressed and point to promising avenues for future research.

A comparative view of the evolution of grasses under domestication

Crop grasses were among the first plants to be domesticated c. 12,000 yr ago, and they still represent the main staple crops for humans. During domestication, as did many other crops, grasses went through dramatic genetic and phenotypic changes. The recent massive increase in genomic data has provided new tools to investigate the genetic basis and consequences of domestication. Beyond the genetics of domestication, many aspects of grass biology, including their phylogeny and developmental biology, are also increasingly well studied, offering a unique opportunity to analyse the domestication process in a comparative way. Taking such a comparative point of view, we review the history of domesticated grasses and how domestication affected their phenotypic and genomic diversity. Considering recent theoretical developments and the accumulation of genetic data, we revisit more specifically the role of mating systems in the domestication process. We close by suggesting future directions for the study of domestication in grasses.

Purging the genome with sexual selection: reducing mutation load through selection on males

Healthy males are likely to have higher mating success than unhealthy males because of differential expression of condition-dependent traits such as mate searching intensity, fighting ability, display vigor, and some types of exaggerated morphological characters. We therefore expect that most new mutations that are deleterious for overall fitness may also be deleterious for male mating success. From this perspective, sexual selection is not limited to influencing those genes directly involved in exaggerated morphological traits but rather affects most, if not all, genes in the genome. If true, sexual selection can be an important force acting to reduce the frequency of deleterious mutations and, as a result, mutation load. We review the literature and find various forms of indirect evidence that sexual selection helps to eliminate deleterious mutations. However, direct evidence is scant, and there are almost no data available to address a key issue: is selection in males stronger than selection in females? In addition, the total effect of sexual selection on mutation load is complicated by possible increases in mutation rate that may be attributable to sexual selection. Finally, sexual selection affects population fitness not only through mutation load but also through sexual conflict, making it difficult to empirically measure how sexual selection affects load. Several lines of enquiry are suggested to better fill large gaps in our understanding of sexual selection and its effect on genetic load.

A mixability theory for the role of sex in evolution

The question of what role sex plays in evolution is still open despite decades of research. It has often been assumed that sex should facilitate the increase in fitness. Hence, the fact that it may break down highly favorable genetic combinations has been seen as a problem. Here, we consider an alternative approach. We define a measure that represents the ability of alleles to perform well across different combinations and, using numerical iterations within a classical population-genetic framework, show that selection in the presence of sex favors this ability in a highly robust manner. We also show that the mechanism responsible for this effect has been out of the purview of previous theory, because it operates during the evolutionary transient, and that the breaking down of favorable genetic combinations is an integral part of it. Implications of these results and more to evolutionary theory are discussed.

Twigs on the tree of life? Neutral and selective models for integrating macroevolutionary patterns with microevolutionary processes in the analysis of asexuality

Neutral models characterize evolutionary or ecological patterns expected in the absence of specific causal processes, such as natural selection or ecological interactions. In this study, we describe and evaluate three neutral models that can, in principle, help to explain the apparent 'twigginess' of asexual lineages on phylogenetic trees without involving the negative consequences predicted for the absence of recombination and genetic exchange between individuals. Previously, such phylogenetic twiggyness of asexual lineages has been uncritically interpreted as evidence that asexuality is associated with elevated extinction rates and thus represents an evolutionary dead end. Our first model uses simple phylogenetic simulations to illustrate that, with sexual reproduction as the ancestral state, low transition rates to stable asexuality, or low rates of ascertained 'speciation' in asexuals, can generate twiggy distributions of asexuality, in the absence of high extinction rates for asexual lineages. The second model, developed by Janko et al. (2008), shows that a dynamic equilibrium between origins and neutral losses of asexuals can, under some conditions, generate a relatively low mean age of asexual lineages. The third model posits that the risk of extinction for asexual lineages may be higher than that of sexuals simply because asexuals inhabit higher latitudes or altitudes, and not due to effects of their reproductive systems. Such neutral models are useful in that they allow quantitative evaluation of whether empirical data, such as phylogenetic and phylogeographic patterns of sex and asexuality, indeed support the idea that asexually reproducing lineages persist over shorter evolutionary periods than sexual lineages, due to such processes as mutation accumulation, slower rates of adaptive evolution, or relatively lower levels of genetic variability.

Endothelin: 20 years from discovery to therapy

Since its identification as an endothelial cell-derived vasoconstrictor peptide in 1988, endothelin-1, the predominant member of the endothelin peptide family, has received considerable interest in basic medical science and in clinical medicine, which is reflected by more than 20 000 scientific publications on endothelin research in the past 20 years. The story of endothelin is unique as the gene sequences of endothelin receptors and the first receptor antagonists became available within only 4 years of the identification of the peptide sequence. The first clinical study in patients with congestive heart failure was published only 3 years thereafter. Yet, despite convincing experimental evidence of a pathogenetic role for endothelin in development, cell function, and disease, many initial clinical studies on endothelin antagonism were negative. In many of these studies, study designs or patient selection were inadequate. Today, for diseases such as pulmonary hypertension, endothelin antagonist treatment has become reality in clinical medicine, and ongoing clinical studies are evaluating additional indications, such as renal disease and cancer. Twenty years after the discovery of endothelin, its inhibitors have finally arrived in the clinical arena and are now providing us with new options to treat disease and prolong the lives of patients. Possible future indications include resistant arterial hypertension, proteinuric renal disease, cancer, and connective tissue diseases.

Sex and deleterious mutations

The evolutionary advantage of sexual reproduction has been considered as one of the most pressing questions in evolutionary biology. While a pluralistic view of the evolution of sex and recombination has been suggested by some, here we take a simpler view and try to quantify the conditions under which sex can evolve given a set of minimal assumptions. Since real populations are finite and also subject to recurrent deleterious mutations, this minimal model should apply generally to all populations. We show that the maximum advantage of recombination occurs for an intermediate value of the deleterious effect of mutations. Furthermore we show that the conditions under which the biggest advantage of sex is achieved are those that produce the fastest fitness decline in the corresponding asexual population and are therefore the conditions for which Muller's ratchet has the strongest effect. We also show that the selective advantage of a modifier of the recombination rate depends on its strength. The quantification of the range of selective effects that favors recombination then leads us to suggest that, if in stressful environments the effect of deleterious mutations is enhanced, a connection between sex and stress could be expected, as it is found in several species.

Female sperm limitation in natural populations of a sexual/asexual mating complex (Poecilia latipinna, Poecilia formosa)

In sperm-dependent sexual/asexual mating systems, male mate choice is critical for understanding the mechanisms behind apparent stability observed in natural populations. The gynogenetic Amazon molly (Poecilia formosa) requires sperm from sexual males (e.g. Poecilia latipinna) to trigger embryogenesis, but inheritance is strictly maternal. Consequently, males should try to avoid or reduce the cost of mating with asexuals. We investigated male mate choice by documenting the presence of sperm in natural populations and found that a higher proportion of sexual females had sperm than asexuals. In addition, among those females that had sperm, sexuals had more sperm than asexuals. Our results hint at a role for male mate choice as a stabilizing factor in such systems.

Localization of the genetic determinants of meiosis suppression in Daphnia pulex

Although approximately 1 in 10,000 animal species is capable of parthenogenetic reproduction, the evolutionary causes and consequences of such transitions remain uncertain. The microcrustacean Daphnia pulex provides a potentially powerful tool for investigating these issues because lineages that are obligately asexual in terms of female function can nevertheless transmit meiosis-suppressing genes to sexual populations via haploid sperm produced by environmentally induced males. The application of association mapping to a wide geographic collection of D. pulex clones suggests that sex-limited meiosis suppression in D. pulex has spread westward from a northeastern glacial refugium, conveyed by a dominant epistatic interaction among the products of at least four unlinked loci, with one entire chromosome being inherited through males in a nearly nonrecombining fashion. With the enormous set of genomic tools now available for D. pulex, these results set the stage for the determination of the functional underpinnings of the conversion of meiosis to a mitotic-like mode of inheritance.

Loss of least-loaded class in asexual populations due to drift and epistasis

We consider the dynamics of a nonrecombining haploid population of finite size that accumulates deleterious mutations irreversibly. This ratchet-like process occurs at a finite speed in the absence of epistasis, but it has been suggested that synergistic epistasis can halt the ratchet. Using a diffusion theory, we find explicit analytical expressions for the typical time between successive clicks of the ratchet for both nonepistatic and epistatic fitness functions. Our calculations show that the interclick time is of a scaling form that in the absence of epistasis gives a speed that is determined by size of the least-loaded class and the selection coefficient. With synergistic interactions, the ratchet speed is found to approach zero rapidly for arbitrary epistasis. Our analytical results are in good agreement with the numerical simulations.

The temporal dynamics of processes underlying Y chromosome degeneration

Y chromosomes originate from ordinary autosomes and degenerate by accumulating deleterious mutations. This accumulation results from a lack of recombination on the Y and is driven by interference among deleterious mutations (Muller's ratchet and background selection) and the fixation of beneficial alleles (genetic hitchhiking). Here I show that the relative importance of these processes is expected to vary over the course of Y chromosome evolution due to changes in the number of active genes. The dominant mode of degeneration on a newly formed gene-rich Y chromosome is expected to be Muller's ratchet and/or background selection due to the large numbers of deleterious mutations arising in active genes. However, the relative importance of these modes of degeneration declines rapidly as active genes are lost. In contrast, the rate of degeneration due to hitchhiking is predicted to be highest on Y chromosomes containing an intermediate number of active genes. The temporal dynamics of these processes imply that a gradual restriction of recombination, as inferred in mammals, will increase the importance of genetic hitchhiking relative to Muller's ratchet and background selection.

Both costs and benefits of sex correlate with relative frequency of asexual reproduction in cyclically parthenogenic Daphnia pulicaria populations

Sexual reproduction is generally believed to yield beneficial effects via the expansion of expressed genetic variation, which increases the efficiency of selection and the adaptive potential of a population. However, when nonadditive gene action is involved, sex can actually impede the adaptive progress of a population. If selection promotes coupling disequilibria between genes of similar effect, recombination and segregation can result in a decrease in expressed genetic variance in the offspring population. In addition, when nonadditive gene action underlies a quantitative trait, sex can produce a change in trait means in a direction opposite to that favored by selection. In this study we measured the change in genotypic trait means and genetic variances across a sexual generation in four populations of the cyclical parthenogen Daphnia pulicaria, which vary predictably in their incidence of sexual reproduction. We show that both the costs and benefits of sex, as measured by changes in means and variances in life-history traits, increase substantially with decreasing frequency of sex.