The ecology of sexual reproduction

Sperm-dependent asexual species and their role in ecology and evolution

Sexual reproduction is the primary mode of reproduction in eukaryotes, but some organisms have evolved deviations from classical sex and switched to asexuality. These asexual lineages have sometimes been viewed as evolutionary dead ends, but recent research has revealed their importance in many areas of general biology. Our review explores the understudied, yet important mechanisms by which sperm-dependent asexuals that produce non-recombined gametes but rely on their fertilization, can have a significant impact on the evolution of coexisting sexual species and ecosystems. These impacts are concentrated around three major fields. Firstly, sperm-dependent asexuals can potentially impact the gene pool of coexisting sexual species by either restricting their population sizes or by providing bridges for interspecific gene flow whose type and consequences substantially differ from gene flow mechanisms expected under sexual reproduction. Secondly, they may impact on sexuals' diversification rates either directly, by serving as stepping-stones in speciation, or indirectly, by promoting the formation of pre- and postzygotic reproduction barriers among nascent species. Thirdly, they can potentially impact on spatial distribution of species, via direct or indirect (apparent) types of competition and Allee effects. For each such mechanism, we provide empirical examples of how natural sperm-dependent asexuals impact the evolution of their sexual counterparts. In particular, we highlight that these broad effects may last beyond the tenure of the individual asexual lineages causing them, which challenges the traditional perception that asexual lineages are short-lived evolutionary dead ends and minor sideshows. Our review also proposes new research directions to incorporate the aforementioned impacts of sperm-dependent asexuals. These research directions will ultimately enhance our understanding of the evolution of genomes and biological interactions in general.

What Ecological Factors Favor Parthenogenesis over Sexual Reproduction? A Study on the Facultatively Parthenogenetic Mayfly Alainites muticus in Natural Populations

AbstractDifferent reproductive modes are characterized by costs and benefits that depend on ecological contexts. For example, sex can provide benefits under complex biotic interactions, while its costs increase under mate limitation. Furthermore, ecological contexts often vary along abiotic gradients. Here, we study how these factors simultaneously influence the frequency of sex in the facultatively parthenogenetic mayfly Alainites muticus. We first verified that parthenogenesis translates into female-biased population sex ratios. We then measured the density of individuals (a proxy for mate limitation) and community diversity (biotic interaction complexity) for 159 A. muticus populations covering a broad altitudinal gradient and used structural equation modeling to investigate their direct and indirect influences on sex ratios. We found no effect of community diversity or altitude on sex ratios. Furthermore, even when females can reproduce parthenogenetically, they generally reproduce sexually, indicating that the benefits of sex exceed its costs in most situations. Sex ratios become female-biased only under low population densities, as expected if mate limitation was the main factor selecting for parthenogenesis. Mate limitation might be widespread in mayflies because of their short adult life span and limited dispersal, which can generate strong selection for reproductive assurance and may provide a stepping stone toward obligate parthenogenesis.

Primate Sex and Its Role in Pleasure, Dominance and Communication

Sexual intercourse in the animal kingdom functions to enable reproduction. However, we now know that several species of non-human primates regularly engage in sex outside of the times when conception is possible. In addition, homosexual and immature sex are not as uncommon as were once believed. This suggests that sex also has important functions outside of reproduction, yet these are rarely discussed in sex-related teaching and research activities concerning primate behaviour. Is the human sexual experience, which includes pleasure, dominance, and communication (among others) unique, or do other primates also share these experiences to any extent? If so, is there any way to measure them, or are they beyond the rigour of scientific objectivity? What would be the evolutionary implications if human-like sexual experiences were found amongst other animals too? We comment on the evidence provided by our close relatives, non-human primates, discuss the affective and social functions of sex, and suggest potential methods for measuring some of these experiences empirically. We hope that this piece may foster the discussion among academics and change the way we think about, teach and research primate sex.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

The advantage of sex: Reinserting fluctuating selection in the pluralist approach

The advantage of sex, and its fixation in some clades and species all over the eukaryote tree of life, is considered an evolutionary enigma, especially regarding its assumed two-fold cost. Several likely hypotheses have been proposed such as (1) a better response to the negative frequency-dependent selection imposed by the “Red Queen” hypothesis; (2) the competition between siblings induced by the Tangled Bank hypothesis; (3) the existence of genetic and of (4) ecological factors that can diminish the cost of sex to less than the standard assumed two-fold; and (5) a better maintenance of genetic diversity and its resulting phenotypic variation, providing a selective advantage in randomly fluctuating environments. While these hypotheses have mostly been studied separately, they can also act simultaneously. This was advocated by several studies which presented a pluralist point of view. Only three among the five causes cited above were considered yet in such a framework: the Red Queen hypothesis, the Tangled Bank and the genetic factors lowering the cost of sex. We thus simulated the evolution of a finite mutating population undergoing negative frequency-dependent selection on phenotypes and a two-fold (or less) cost of sexuality, experiencing randomly fluctuating selection along generations. The individuals inherited their reproductive modes, either clonal or sexual. We found that exclusive sexuality begins to fix in populations exposed to environmental variation that exceeds the width of one ecological niche (twice the standard deviation of a Gaussian response to environment). This threshold was lowered by increasing negative frequency-dependent selection and when reducing the two-fold cost of sex. It contributes advocating that the different processes involved in a short-term advantage of sex and recombination can act in combination to favor the fixation of sexual reproduction in populations.

Genetic diversity and disease: The past, present, and future of an old idea

Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.

Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa

Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.

Major Evolutionary Transitions and the Roles of Facilitation and Information in Ecosystem Transformations

A small number of extraordinary “Major Evolutionary Transitions” (METs) have attracted attention among biologists. They comprise novel forms of individuality and information, and are defined in relation to organismal complexity, irrespective of broader ecosystem-level effects. This divorce between evolutionary and ecological consequences qualifies unicellular eukaryotes, for example, as a MET although they alone failed to significantly alter ecosystems. Additionally, this definition excludes revolutionary innovations not fitting into either MET type (e.g., photosynthesis). We recombine evolution with ecology to explore how and why entire ecosystems were newly created or radically altered – as Major System Transitions (MSTs). In doing so, we highlight important morphological adaptations that spread through populations because of their immediate, direct-fitness advantages for individuals. These are Major Competitive Transitions, or MCTs. We argue that often multiple METs and MCTs must be present to produce MSTs. For example, sexually-reproducing, multicellular eukaryotes (METs) with anisogamy and exoskeletons (MCTs) significantly altered ecosystems during the Cambrian. Therefore, we introduce the concepts of Facilitating Evolutionary Transitions (FETs) and Catalysts as key events or agents that are insufficient themselves to set a MST into motion, but are essential parts of synergies that do. We further elucidate the role of information in MSTs as transitions across five levels: (I) Encoded; (II) Epigenomic; (III) Learned; (IV) Inscribed; and (V) Dark Information. The latter is ‘authored’ by abiotic entities rather than biological organisms. Level IV has arguably allowed humans to produce a MST, and V perhaps makes us a FET for a future transition that melds biotic and abiotic life into one entity. Understanding the interactive processes involved in past major transitions will illuminate both current events and the surprising possibilities that abiotically-created information may produce.

Direct evidence of sex and a hypothesis about meiosis in Symbiodiniaceae

Dinoflagellates in the family Symbiodiniaceae are obligate endosymbionts of diverse marine invertebrates, including corals, and impact the capacity of their hosts to respond to climate change-driven ocean warming. Understanding the conditions under which increased genetic variation in Symbiodiniaceae arises via sexual recombination can support efforts to evolve thermal tolerance in these symbionts and ultimately mitigate coral bleaching, the breakdown of the coral-Symbiodiniaceae partnership under stress. However, direct observations of meiosis in Symbiodiniaceae have not been reported, despite various lines of indirect evidence that it occurs. We present the first cytological evidence of sex in Symbiodiniaceae based on nuclear DNA content and morphology using Image Flow Cytometry, Cell Sorting and Confocal Microscopy. We show the Symbiodiniaceae species, Cladocopium latusorum, undergoes gamete conjugation, zygote formation, and meiosis within a dominant reef-building coral in situ. On average, sex was detected in 1.5% of the cells analyzed (N = 10,000-40,000 cells observed per sample in a total of 20 samples obtained from 3 Pocillopora colonies). We hypothesize that meiosis follows a two-step process described in other dinoflagellates, in which diploid zygotes form dyads during meiosis I, and triads and tetrads as final products of meiosis II. This study sets the stage for investigating environmental triggers of Symbiodiniaceae sexuality and can accelerate the assisted evolution of a key coral symbiont in order to combat reef degradation.

Density, parasitism, and sexual reproduction are strongly correlated in lake Daphnia populations

Many organisms can reproduce both asexually and sexually. For cyclical parthenogens, periods of asexual reproduction are punctuated by bouts of sexual reproduction, and the shift from asexual to sexual reproduction has large impacts on fitness and population dynamics. We studied populations of Daphnia dentifera to determine the amount of investment in sexual reproduction as well as the factors associated with variation in investment in sex. To do so, we tracked host density, infections by nine different parasites, and sexual reproduction in 15 lake populations of D. dentifera for 3 years. Sexual reproduction was seasonal, with male and ephippial female production beginning as early as late September and generally increasing through November. However, there was substantial variation in the prevalence of sexual individuals across populations, with some populations remaining entirely asexual throughout the study period and others shifting almost entirely to sexual females and males. We found strong relationships between density, prevalence of infection, parasite species richness, and sexual reproduction in these populations. However, strong collinearity between density, parasitism, and sexual reproduction means that further work will be required to disentangle the causal mechanisms underlying these relationships.

Reproduction in Trypanosomatids: Past and Present

Simple Summary

The reproduction of trypanosomatids is a fundamental issue for host–parasite interaction, and its biological importance lies in knowing how these species acquire new defense mechanisms against the countermeasures imposed by the host, which is consistent with the theory of the endless race or the Red Queen hypothesis for the existence of meiotic sex. Moreover, the way these species re-produce may also be at the origin of novel and more virulent clades and is relevant from a thera-peutic or vaccination point of view, as sex may contribute to increased tolerance and even to the rapid acquisition of drug resistance mechanisms. Kinetoplastids are single-celled organisms, many of them being responsible for important parasitic diseases, globally termed neglected diseases, which are endemic in low-income countries. Leishmaniasis, African (sleeping sickness) and American trypanosomiasis (Chagas disease) caused by trypanosomatids are among the most ne-glected tropical scourges related to poverty and poor health systems. The reproduction of these microorganisms has long been considered to be clonal due to population genetic observations. However, there is increasing evidence of true sex and genetic exchange events under laboratory conditions. We would like to highlight the importance of this topic in the field of host/parasite in-terplay, virulence, and drug resistance.

Abstract

Diseases caused by trypanosomatids (Sleeping sickness, Chagas disease, and leishmaniasis) are a serious public health concern in low-income endemic countries. These diseases are produced by single-celled parasites with a diploid genome (although aneuploidy is frequent) organized in pairs of non-condensable chromosomes. To explain the way they reproduce through the analysis of natural populations, the theory of strict clonal propagation of these microorganisms was taken as a rule at the beginning of the studies, since it partially justified their genomic stability. However, numerous experimental works provide evidence of sexual reproduction, thus explaining certain naturally occurring events that link the number of meiosis per mitosis and the frequency of mating. Recent techniques have demonstrated genetic exchange between individuals of the same species under laboratory conditions, as well as the expression of meiosis specific genes. The current debate focuses on the frequency of genomic recombination events and its impact on the natural parasite population structure. This paper reviews the results and techniques used to demonstrate the existence of sex in trypanosomatids, the inheritance of kinetoplast DNA (maxi- and minicircles), the impact of genetic exchange in these parasites, and how it can contribute to the phenotypic diversity of natural populations.

Fixation of allelic gene expression landscapes and expression bias pattern shape the transcriptome of the clonal Amazon molly

The Amazon molly is a unique clonal fish species that originated from an interspecies hybrid between Poecilia species P. mexicana and P. latipinna. It reproduces by gynogenesis, which eliminates paternal genomic contribution to offspring. An earlier study showed that Amazon molly shows biallelic expression for a large portion of the genome, leading to two main questions: (1) Are the allelic expression patterns from the initial hybridization event stabilized or changed during establishment of the asexual species and its further evolution? (2) Is allelic expression biased toward one parental allele a stochastic or adaptive process? To answer these questions, the allelic expression of P. formosa siblings was assessed to investigate intra- and inter-cohort allelic expression variability. For comparison, interspecies hybrids between P. mexicana and P. latipinna were produced in the laboratory to represent the P. formosa ancestor. We have identified inter-cohort and intra-cohort variation in parental allelic expression. The existence of inter-cohort divergence suggests functional P. formosa allelic expression patterns do not simply reflect the atavistic situation of the first interspecies hybrid but potentially result from long-term selection of transcriptional fitness. In addition, clonal fish show a transcriptional trend representing minimal intra-clonal variability in allelic expression patterns compared to the corresponding hybrids. The intra-clonal similarity in gene expression translates to sophisticated genetic functional regulation at the individuum level. These findings suggest the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals.

Antagonistic species interaction drives selection for sex in a predator-prey system

The evolutionary maintenance of sexual reproduction has long challenged biologists as the majority of species reproduce sexually despite inherent costs. Providing a general explanation for the evolutionary success of sex has thus proven difficult and resulted in numerous hypotheses. A leading hypothesis suggests that antagonistic species interaction can generate conditions selecting for increased sex due to the production of rare or novel genotypes that are beneficial for rapid adaptation to recurrent environmental change brought on by antagonism. To test this ecology-based hypothesis, we conducted experimental evolution in a predator (rotifer)-prey (algal) system by using continuous cultures to track predator-prey dynamics and in situ rates of sex in the prey over time and within replicated experimental populations. Overall, we found that predator-mediated fluctuating selection for competitive versus defended prey resulted in higher rates of genetic mixing in the prey. More specifically, our results showed that fluctuating population sizes of predator and prey, coupled with a trade-off in the prey, drove the sort of recurrent environmental change that could provide a benefit to sex in the prey, despite inherent costs. We end with a discussion of potential population genetic mechanisms underlying increased selection for sex in this system, based on our application of a general theoretical framework for measuring the effects of sex over time, and interpreting how these effects can lead to inferences about the conditions selecting for or against sexual reproduction in a system with antagonistic species interaction.

Asexual parasites and their extraordinary host ranges

In diverse parasite taxa, from scale insects to root-knot nematodes, asexual lineages have exceptionally large host ranges, larger than those of their sexual relatives. Phylogenetic comparative studies of parasite taxa indicate that increases in host range and geographic range increase the probability of establishment of asexual lineages. At first pass, this convergence of traits appears counter-intuitive: intimate, antagonistic association with an enormous range of host taxa correlates with asexual reproduction, which should limit genetic variation within populations. Why would narrow host ranges favor sexual parasites and large host ranges favor asexual parasites? To take on this problem I link theory on ecological specialization to the two predominant hypotheses for the evolution of sex. I argue that both hypotheses predict a positive association between host range and the probability of invasion of asexual parasites, mediated either by variation in population size or in the strength of antagonistic coevolution. I also review hypotheses on colonization and the evolution of niche breadth in asexual lineages. I emphasize parasite taxa, with their diversity of reproductive modes and ecological strategies, as valuable assets in the hunt for solutions to the classic problems of the evolution of sex and geographic parthenogenesis.

Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation

The evolution of predominant self-fertilisation frequently coincides with the evolution of a collection of phenotypes that comprise the 'selfing syndrome', in both plants and animals. Genomic features also display a selfing syndrome. Selfing syndrome traits often involve changes to male and female reproductive characters that were subject to sexual selection and sexual conflict in the obligatorily outcrossing ancestor, including the gametic phase for both plants and animals. Rapid evolution of reproductive traits, due to both relaxed selection and directional selection under the new status of predominant selfing, lays the genetic groundwork for reproductive isolation. Consequently, shifts in sexual selection pressures coupled to transitions to selfing provide a powerful paradigm for investigating the speciation process. Plant and animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: genetic transmission advantage to selfing or reproductive assurance outweighing the costs of inbreeding depression vs the costs of males and meiosis. Here, I synthesise links between sexual selection, evolution of selfing and speciation, with particular focus on identifying commonalities and differences between plant and animal systems and pointing to areas warranting further synergy.

Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes

Males of Caenorhabditis elegans provide a crucial practical tool in the laboratory, but, as the rarer and more finicky sex, have not enjoyed the same depth of research attention as hermaphrodites. Males, however, have attracted the attention of evolutionary biologists who are exploiting the C. elegans system to test longstanding hypotheses about sexual selection, sexual conflict, transitions in reproductive mode, and genome evolution, as well as to make new discoveries about Caenorhabditis organismal biology. Here, we review the evolutionary concepts and data informed by study of males of C. elegans and other Caenorhabditis We give special attention to the important role of sperm cells as a mediator of inter-male competition and male-female conflict that has led to drastic trait divergence across species, despite exceptional phenotypic conservation in many other morphological features. We discuss the evolutionary forces important in the origins of reproductive mode transitions from males being common (gonochorism: females and males) to rare (androdioecy: hermaphrodites and males) and the factors that modulate male frequency in extant androdioecious populations, including the potential influence of selective interference, host-pathogen coevolution, and mutation accumulation. Further, we summarize the consequences of males being common vs rare for adaptation and for trait divergence, trait degradation, and trait dimorphism between the sexes, as well as for molecular evolution of the genome, at both micro-evolutionary and macro-evolutionary timescales. We conclude that C. elegans male biology remains underexploited and that future studies leveraging its extensive experimental resources are poised to discover novel biology and to inform profound questions about animal function and evolution.

Abandoning the ship using sex, dispersal or dormancy: multiple escape routes from challenging conditions

Natural populations often experience environments that vary across space and over time, leading to spatio-temporal variation of the fitness of a genotype. If local conditions are poor, organisms can disperse in space (physical movement) or time (dormancy, diapause). Facultatively sexual organisms can switch between asexual and sexual reproduction, and thus have a third option available to deal with maladaptedness: they can engage in sexual reproduction in unfavourable conditions (an 'abandon-ship' response). Sexual reproduction in facultatively sexual organisms is often coupled with dispersal and/or dormancy, while bet-hedging theory at first sight predicts sex, dispersal and dormancy to covary negatively, as they represent different escape mechanisms that could substitute for each other. Here we briefly review the observed links between sex, dormancy and dispersal, and model the expected covariation patterns of dispersal, dormancy and the reproductive mode in the context of local adaptation to spatio-temporally fluctuating environments. The correlations between sex, dormancy and dispersal evolve differently within species versus across species. Various risk-spreading strategies are not completely interchangeable, as each has dynamic consequences that can feed back into the profitability of others. Our results shed light on the discrepancy between previous theoretical predictions on covarying risk-spreading traits and help explain why sex often associates with other means of escaping unfavourable situations.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.

Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish

Parasite-mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of long-term self-fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host's ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MS-AFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a predomintanly self-fertilizing fish, to analyze the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.

Reproductive differences among species, and between individuals and cohorts, in the leech genus Helobdella (Lophotrochozoa; Annelida; Clitellata; Hirudinida; Glossiphoniidae), with implications for reproductive resource allocation in hermaphrodites

Leeches and oligochaetes comprise a monophyletic group of annelids, the Clitellata, whose reproduction is characterized by simultaneous hermaphroditism. While most clitellate species reproduce by cross-fertilization, self-fertilization has been described within the speciose genus Helobdella. Here we document the reproductive life histories and reproductive capacities for three other Helobdella species. Under laboratory conditions, both H. robusta and H. octatestisaca exhibit uniparental reproduction, apparently reflecting self-fertility, and suggesting that this trait is ancestral for the genus. However, the third species, H. austinensis, seems incapable of reproduction by self-fertilization, so we inferred its reproductive life history by analyzing reproduction in breeding cohorts. Comparing the reproductive parameters for H. robusta reproducing in isolation and in cohorts revealed that reproduction in cohorts is dramatically delayed with respect to that of isolated individuals, and that cohorts of leeches coordinate their cocoon deposition in a manner that is not predicted from the reproductive parameters of individuals reproducing in isolation. Finally, our comparisons of reproductive capacity for individuals versus cohorts for H. robusta, and between different sizes of cohorts for H. austinensis, reveal differences in resource allocation between male and female reproductive roles that are consistent with evolutionary theory.

High-resolution insight into recombination events at the SD1 locus in rice

Recombination during meiosis plays an important role in genome evolution by reshuffling existing genetic variations into fresh combinations with the possibility of recovery of lost ancestral genotypes. While crossover (CO) events have been well studied, gene conversion events (GCs), which represent non-reciprocal information transfer between chromosomes, are poorly documented and difficult to detect due to their relatively small converted tract size. Here, we document these GC events and their phenotypic effects at an important locus in rice containing the SD1 gene, where multiple defective alleles contributed to the semi-dwarf phenotype of rice in the 'Green Revolution' of the 1960s. Here, physical separation of two defects allows recombination to generate the wild-type SD1 gene, for which plant height can then be used as a reporter. By screening 18 000 F₂ progeny from a cross between two semi-dwarf cultivars that carry these different defective alleles, we detected 24 GC events, indicating a conversion rate of ~3.3 × 10^-4 per marker per generation in a single meiotic cycle in rice. Furthermore, our data show that indels and single-nucleotide polymorphisms (SNPs) do not differ significantly in GC rates, at least at the SD1 locus. Our results provide strong evidence that GC by itself can regain an ancestral phenotype that was lost through mutation. This GC detection approach is likely to be broadly applicable to natural or artificial alleles of other phenotype-related functional genes, which are abundant in other plant genomes.

The effect of parasite infection on the recombination rate of the mosquito Aedes aegypti

Sexual reproduction and meiotic recombination generate new genetic combinations and may thereby help an individual infected by a parasite to protect its offspring from being infected. While this idea is often used to understand the evolutionary forces underlying the maintenance of sex and recombination, it also suggests that infected individuals should increase plastically their rate of recombination. We tested the latter idea with the mosquito Aedes aegypti and asked whether females infected by the microsporidian Vavraia culicis were more likely to have recombinant offspring than uninfected females. To measure the rate of recombination over a chromosome we analysed combinations of microsatellites on chromosome 3 in infected and uninfected females, in the (uninfected) males they copulated with and in their offspring. As predicted, the infected females were more likely to have recombinant offspring than the uninfected ones. These results show the ability of a female to diversify her offspring in response to parasitic infection by plastically increasing her recombination rate.

Turnover in local parasite populations temporarily favors host outcrossing over self-fertilization during experimental evolution

The ubiquity of outcrossing in plants and animals is difficult to explain given its costs relative to self-fertilization. Despite these costs, exposure to changing environmental conditions can temporarily favor outcrossing over selfing. Therefore, recurring episodes of environmental change are predicted to favor the maintenance of outcrossing. Studies of host-parasite coevolution have provided strong support for this hypothesis. However, it is unclear whether multiple exposures to novel parasite genotypes in the absence of coevolution are sufficient to favor outcrossing. Using the nematode Caenorhabditis elegans and the bacterial parasite Serratia marcescens, we studied host responses to parasite turnover. We passaged several replicates of a host population that was well-adapted to the S. marcescens strain Sm2170 with either Sm2170 or one of three novel S. marcescens strains, each derived from Sm2170, for 18 generations. We found that hosts exposed to novel parasites maintained higher outcrossing rates than hosts exposed to Sm2170. Nonetheless, host outcrossing rates declined over time against all but the most virulent novel parasite strain. Hosts exposed to the most virulent novel strain exhibited increased outcrossing rates for approximately 12 generations, but did not maintain elevated levels of outcrossing throughout the experiment. Thus, parasite turnover can transiently increase host outcrossing. These results suggest that recurring episodes of parasite turnover have the potential to favor the maintenance of host outcrossing. However, such maintenance may require frequent exposure to novel virulent parasites, rapid rates of parasite turnover, and substantial host gene flow.

Sex in the wild: How and why field-based studies contribute to solving the problem of sex

Why and how sexual reproduction is maintained in natural populations, the so-called "queen of problems," is a key unanswered question in evolutionary biology. Recent efforts to solve the problem of sex have often emphasized results generated from laboratory settings. Here, we use a survey of representative "sex in the wild" literature to review and synthesize the outcomes of empirical studies focused on natural populations. Especially notable results included relatively strong support for mechanisms involving niche differentiation and a near absence of attention to adaptive evolution. Support for a major role of parasites is largely confined to a single study system, and only three systems contribute most of the support for mutation accumulation hypotheses. This evidence for taxon specificity suggests that outcomes of particular studies should not be more broadly extrapolated without extreme caution. We conclude by suggesting steps forward, highlighting tests of niche differentiation mechanisms in both laboratory and nature, and empirical evaluation of adaptive evolution-focused hypotheses in the wild. We also emphasize the value of leveraging the growing body of genomic resources for nonmodel taxa to address whether the clearance of harmful mutations and spread of beneficial variants in natural populations proceeds as expected under various hypotheses for sex.

Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly

The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.

Evolution of Caenorhabditis elegans host defense under selection by the bacterial parasite Serratia marcescens

Parasites can impose strong selection on hosts. In response, some host populations have adapted via the evolution of defenses that prevent or impede infection by parasites. However, host populations have also evolved life history shifts that maximize host fitness despite infection. Outcrossing and self-fertilization can have contrasting effects on evolutionary trajectories of host populations. While selfing and outcrossing are known to affect the rate at which host populations adapt in response to parasites, these mating systems may also influence the specific traits that underlie adaptation to parasites. Here, we determined the role of evolved host defense versus altered life history,in mixed mating (selfing and outcrossing) and obligately outcrossing C. elegans host populations after experimental evolution with the bacterial parasite, S. marcescens. Similar to previous studies, we found that both mixed mating and obligately outcrossing host populations adapted to S. marcescens exposure, and that the obligately outcrossing populations exhibited the greatest rates of adaptation. Regardless of the host population mating system, exposure to parasites did not significantly alter reproductive timing or total fecundity over the course of experimental evolution. However, both mixed mating and obligately outcrossing host populations exhibited significantly reduced mortality rates in the presence of the parasite after experimental evolution. Therefore, adaptation in both the mixed mating and obligately outcrossing populations was driven, at least in part, by the evolution of increased host defense and not changes in host life history. Thus, the host mating system altered the rate of adaptation, but not the nature of adaptive change in the host populations.

How counterfactuals of Red-Queen theory shed light on science and its historiography

A historical episode of evolutionary theory, which has lead to the Red Queen theory of the evolutionary maintenance of sex, includes two striking contingencies. These are used to explore alternative what-if scenarios, in order to test some common opinions about such counterfactuals. This sheds new light on the nature of science and its historiography. One counterfactual leads to an unexpected convergence of its result to that of the actual science but, nevertheless, differs in its causal structure. The other diverges towards an incompatible alternative, but this requires further contingent choices that also diverge from actual science. The convergence in the first counterfactual is due to a horizontal transfer of knowledge. Similar transfers of knowledge are typical for innovations of actual science. This suggests that contingent choices can merge as well as fork research traditions both in actual research and counterfactual history. Neither the paths of the actual history of science nor those of its counterfactual alternatives will form a tree of exclusively diverging bifurcations, but a network instead. Convergencies in counterfactuals may, therefore, be due to the web-structure of science as much as to the aims of the historians in question. Furthermore, the difference in causal structure between the actual science and its convergent counterfactual might become diagnostic for external factors rather than internal aims forcing a historian towards convergence.

Host mating system and coevolutionary dynamics shape the evolution of parasite avoidance in Caenorhabditis elegans host populations

Hosts exhibit a variety of defence mechanisms against parasites, including avoidance. Both host–parasite coevolutionary dynamics and the host mating system can alter the evolutionary trajectories of populations. Does the nature of host–parasite interactions and the host mating system affect the mechanisms that evolve to confer host defence? In a previous experimental evolution study, mixed mating and obligately outcrossing Caenorhabditis elegans host populations adapted to either coevolving or static Serratia marcescens parasite populations. Here, we assessed parasite avoidance as a mechanism underlying host adaptation. We measured host feeding preference for the coevolved and static parasites vs preference for Escherichia coli, to assess the evolution of avoidance behaviour within our experiment. We found that mixed mating host populations evolved a preference for E. coli relative to the static parasite strain; therefore, the hosts evolved parasite avoidance as a defence. However, mixed mating hosts did not exhibit E. coli preference when exposed to coevolved parasites, so avoidance cannot account for host adaptation to coevolving parasites. Further, the obligately outcrossing host populations did not exhibit parasite avoidance in the presence of either static or coevolved parasites. Therefore, both the nature of host–parasite interactions and the host mating system shaped the evolution of host defence.

The Natural Biotic Environment of Caenorhabditis elegans

Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism's biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ∼10 yr ago. Since then, an increasing number of studies have focused on the nematode's natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information on the natural environment of C. elegans We focus on the biotic environment, which is usually less predictable and thus can create high selective constraints that are likely to have had a strong impact on C. elegans evolution. This nematode is particularly abundant in microbe-rich environments, especially rotting plant matter such as decomposing fruits and stems. In this environment, it is part of a complex interaction network, which is particularly shaped by a species-rich microbial community. These microbes can be food, part of a beneficial gut microbiome, parasites and pathogens, and possibly competitors. C. elegans is additionally confronted with predators; it interacts with vector organisms that facilitate dispersal to new habitats, and also with competitors for similar food environments, including competitors from congeneric and also the same species. Full appreciation of this nematode's biology warrants further exploration of its natural environment and subsequent integration of this information into the well-established laboratory-based research approaches.

Patterns and mechanisms in instances of endosymbiont-induced parthenogenesis

Female-producing parthenogenesis can be induced by endosymbionts that increase their transmission by manipulating host reproduction. Our literature survey indicates that such endosymbiont-induced parthenogenesis is known or suspected in 124 host species from seven different arthropod taxa, with Wolbachia as the most frequent endosymbiont (in 56-75% of host species). Most host species (81%, 100 out of 124) are characterized by haplo-diploid sex determination, but a strong ascertainment bias likely underestimates the frequency of endosymbiont-induced parthenogenesis in hosts with other sex determination systems. In at least one taxon, hymenopterans, endosymbionts are a significant driver of transitions from sexual to parthenogenetic reproduction, with one-third of lineages being parthenogenetic as a consequence of endosymbiont infection. Endosymbiont-induced parthenogenesis appears to facilitate the maintenance of reproductive polymorphism: at least 50% of species comprise both sexual (uninfected) and parthenogenetic (infected) strains. These strains feature distribution differences similar to the ones documented for lineages with genetically determined parthenogenesis, with endosymbiont-induced parthenogens occurring at higher latitudes than their sexual relatives. Finally, although gamete duplication is often considered as the main mechanism for endosymbiont-induced parthenogenesis, it underlies parthenogenesis in only half of the host species studied thus far. We point out caveats in the methods used to test for endosymbiont-induced parthenogenesis and suggest specific approaches that allow for firm conclusions about the involvement of endosymbionts in the origin of parthenogenesis.

Hill-Robertson interference maintained by Red Queen dynamics favours the evolution of sex

Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genomewide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination. This theory has received only limited support. However, Red Queen dynamics without epistasis may provide the ecological conditions that maintain strong and frequent selective interference in finite populations that indirectly selects for recombination. This hypothesis is developed here through the simulation of Red Queen dynamics. This approach required the development of a method to calculate the exact frequencies of multilocus haplotypes after recombination. Simulations show that recombination is favoured by the moderately weak selection of many loci involved in the interaction between a host and its parasites, which results in substitution rates that are compatible with empirical estimates. The model also reproduces the previously reported rapid increase in the rate of outcrossing in Caenorhabditis elegans coevolving with a bacterial pathogen.

Factors affecting egg production in the selfing mangrove rivulus (Kryptolebias marmoratus)

The mangrove rivulus, Kryptolebias marmoratus, is one of two known vertebrate species with preferentially self-fertilizing hermaphrodites. Males also exist, and can outcross with hermaphrodites. Outcrossing events vary across wild populations and occur infrequently in laboratory settings. This study sought to add dimension to our understanding of mangrove rivulus reproductive habits by probing the effects of male presence on hermaphroditic unfertilized egg production. Specifically, we quantified egg production of solitary hermaphrodites compared to hermaphrodites exposed to males and exposed to other hermaphrodites. Hermaphrodites tended to produce more fertilized eggs in the presence of males but unfertilized eggs were produced relatively rarely and did not vary significantly among treatments. The probability that hermaphrodites would produce eggs changed as a function of genetic dissimilarity with their partner and in a season-dependent manner. In the fall, the probability of laying eggs decreased as a function of increased genetic dissimilarity, regardless of the sex of the partner. In the winter/spring, however, the probability of laying eggs increased markedly with increased genetic dissimilarity, regardless of the sex of the partner. Our findings indicate that reproductive decisions are modulated by factors beyond male presence, and we discuss a number of alternative hypotheses that should be tested in future studies.

The effect of sex on the repeatability of evolution in different environments

The adaptive function of sex has been extensively studied, while less consideration has been given to the potential downstream consequences of sex on evolution. Here, we investigate one such potential consequence, the effect of sex on the repeatability of evolution. By affecting the repeatability of evolution, sex could have important implications for biodiversity, and for our ability to make predictions about the outcome of environmental change. We allowed asexual and sexual populations of Chlamydomonas reinhardtii to evolve in novel environments and monitored both their change in fitness and variance in fitness after evolution. Sex affected the repeatability of evolution by changing the importance of the effect of selection, chance, and ancestral constraints on the outcome of the evolutionary process. In particular, the effects of sex were highly dependent on the initial genetic composition of the population and on the environment. Given the lack of a consistent effect of sex on repeatability across the environments used here, further studies to dissect in more detail the underlying reasons for these differences as well as studies in additional environments are required if we are to have a general understanding of the effects of sex on the repeatability of evolution.

The Integral Role of Genetic Variation in the Evolution of Outcrossing in the Caenorhabditis elegans-Serratia marcescens Host-Parasite System

Outcrossing is predicted to facilitate more rapid adaptation than self-fertilization as a result of genetic exchange between genetically variable individuals. Such genetic exchange may increase the efficacy of selection by breaking down Hill-Robertson interference, as well as promoting the maintenance of within-lineage genetic diversity. Experimental studies have demonstrated the selective advantage of outcrossing in novel environments. Here, we assess the specific role of genetic variation in the evolution of outcrossing. We experimentally evolved genetically variable and inbred populations of mixed mating (outcrossing and self-fertilizing) Caenorhabditis elegans nematodes under novel ecological conditions—specifically the presence of the virulent parasite Serratia marcescens. Outcrossing rates increased in genetically variable host populations evolved in the presence of the parasite, whereas parasite exposure in inbred populations resulted in reduced rates of host outcrossing. The host populations with genetic variation also exhibited increased fitness in the presence of the parasite over eight generations, whereas inbred populations did not. This increase in fitness was primarily the result of adaptation to the parasite, rather than recovery from initial inbreeding depression. Therefore, the benefits of outcrossing were only manifested in the presence of genetic variation, and outcrossing was favored over self-fertilization as a result. As predicted, the benefits of outcrossing under novel ecological conditions are a product of genetic exchange between genetically diverse lineages.

Nematode-bacteria mutualism: Selection within the mutualism supersedes selection outside of the mutualism

The coevolution of interacting species can lead to codependent mutualists. Little is known about the effect of selection on partners within verses apart from the association. Here, we determined the effect of selection on bacteria (Xenorhabdus nematophila) both within and apart from its mutualistic partner (a nematode, Steinernema carpocapsae). In nature, the two species cooperatively infect and kill arthropods. We passaged the bacteria either together with (M+), or isolated from (M-), nematodes under two different selection regimes: random selection (S-) and selection for increased virulence against arthropod hosts (S+). We found that the isolated bacteria evolved greater virulence under selection for greater virulence (M-S+) than under random selection (M-S-). In addition, the response to selection in the isolated bacteria (M-S+) caused a breakdown of the mutualism following reintroduction to the nematode. Finally, selection for greater virulence did not alter the evolutionary trajectories of bacteria passaged within the mutualism (M+S+ = M+S-), indicating that selection for the maintenance of the mutualism was stronger than selection for increased virulence. The results show that selection on isolated mutualists can rapidly breakdown beneficial interactions between species, but that selection within a mutualism can supersede external selection, potentially generating codependence over time.

Evolutionary responses to climate change in parasitic systems

Species may respond to climate change in many ecological and evolutionary ways. In this simulation study, we focus on the concurrent evolution of three traits in response to climate change, namely dispersal probability, temperature tolerance (or niche width), and temperature preference (optimal habitat). More specifically, we consider evolutionary responses in host species involved in different types of interaction, that is parasitism or commensalism, and for low or high costs of a temperature tolerance-fertility trade-off (cost of generalization). We find that host species potentially evolve all three traits simultaneously in response to increasing temperature but that the evolutionary response interacts and may be compensatory depending on the conditions. The evolutionary adjustment of temperature preference is slower in the parasitism than in commensalism scenario. Parasitism, in turn, selects for higher temperature tolerance and increased dispersal. High costs for temperature tolerance (i.e. generalization) restrict evolution of tolerance and thus lead to a faster response in temperature preference than that observed under low costs. These results emphasize the possible role of biotic interactions and the importance of 'multidimensional' evolutionary responses to climate change.

Mitochondrial maintenance failure in aging and role of sexual dimorphism

Gene expression changes during aging are partly conserved across species, and suggest that oxidative stress, inflammation and proteotoxicity result from mitochondrial malfunction and abnormal mitochondrial-nuclear signaling. Mitochondrial maintenance failure may result from trade-offs between mitochondrial turnover versus growth and reproduction, sexual antagonistic pleiotropy and genetic conflicts resulting from uni-parental mitochondrial transmission, as well as mitochondrial and nuclear mutations and loss of epigenetic regulation. Aging phenotypes and interventions are often sex-specific, indicating that both male and female sexual differentiation promote mitochondrial failure and aging. Studies in mammals and invertebrates implicate autophagy, apoptosis, AKT, PARP, p53 and FOXO in mediating sex-specific differences in stress resistance and aging. The data support a model where the genes Sxl in Drosophila, sdc-2 in Caenorhabditis elegans, and Xist in mammals regulate mitochondrial maintenance across generations and in aging. Several interventions that increase life span cause a mitochondrial unfolded protein response (UPRmt), and UPRmt is also observed during normal aging, indicating hormesis. The UPRmt may increase life span by stimulating mitochondrial turnover through autophagy, and/or by inhibiting the production of hormones and toxic metabolites. The data suggest that metazoan life span interventions may act through a common hormesis mechanism involving liver UPRmt, mitochondrial maintenance and sexual differentiation.

A phylogenetic test of the Red Queen Hypothesis: outcrossing and parasitism in the Nematode phylum

Sexual outcrossing is costly relative to selfing and asexuality, yet it is ubiquitous in nature, a paradox that has long puzzled evolutionary biologists. The Red Queen Hypothesis argues that outcrossing is maintained by antagonistic interactions between host and parasites. Most tests of this hypothesis focus on the maintenance of outcrossing in hosts. The Red Queen makes an additional prediction that parasitic taxa are more likely to be outcrossing than their free-living relatives. We test this prediction in the diverse Nematode phylum using phylogenetic comparative methods to evaluate trait correlations. In support of the Red Queen, we demonstrate a significant correlation between parasitism and outcrossing in this clade. We find that this correlation is driven by animal parasites, for which outcrossing is significantly enriched relative to both free-living and plant parasitic taxa. Finally, we test hypotheses for the evolutionary history underlying the correlation of outcrossing and animal parasitism. Our results demonstrate that selfing and asexuality are significantly less likely to arise on parasitic lineages than on free-living ones. The findings of this study are consistent with the Red Queen Hypothesis. Moreover, they suggest that the maintenance of genetic variation is an important factor in the persistence of parasitic lineages.