Evolution Letters

The phenotypic effects of mutations often depend on the genetic background, yet general patterns remain poorly resolved. Here, we tested whether genotypes drawn from the same natural population, but differing in their breeding values for a polygenic trait, differed in their contribution of new mutational variation to that trait. We established >200 mutation-accumulation (MA) lines from four Drosophila serrata genotypes. Analysing >44,000 wing-size measurements, collected over 30 generations, we quantified mutational variance and mutational bias for size. Genotypes with the smallest and largest breeding values for size contributed similar (statistically indistinguishable) amounts of mutational variance. In contrast, the genotype with an intermediate breeding value exhibited remarkably low (statistically undetectable) mutational variance, low micro-environmental variance, and high line survival over time, consistent with limited mutational decay in fitness. The three genotypes with detectable mutational input showed declines in mean size over time, indicating a consistent mutational bias toward smaller size, as reported in other taxa. The magnitude of this bias appeared genotype dependent, with the MA populations founded from the larger ancestors declining nearly twice as fast as that founded from the smallest ancestor. Together, these results demonstrate substantial heterogeneity in mutational properties among genotypes within a single natural population where the trait value spans a relatively narrow range. Such genotype-specific mutational input is expected to shape both the standing genetic variance and the evolutionary trajectory of polygenic traits.

The evolution of plant resistance naturally occurs in complex, multifaceted environments that consist of multiple simultaneous stressors. Understanding how shifting environmental contexts may shape resistance evolution requires empirical studies that consider the combined effects of interacting stressors on fitness and selection. Here, we examined how exposure to an insecticide impacts the evolution of resistance to the herbicide glyphosate in Ipomoea purpurea (common morning glory). Through a factorial field experiment, we manipulated glyphosate and an insecticide to estimate selection on glyphosate and herbivory resistance. We found that glyphosate acted as the primary agent of selection, favoring higher levels of glyphosate resistance. In the presence of glyphosate alone, positive correlational selection favored a combination of higher glyphosate and herbivory resistance, supporting prior work that suggested these traits may be linked. Importantly, insecticide exposure modified both glyphosate resistance and the strength of selection acting upon the trait by increasing resistance and weakening selection. Together, our results indicate that the evolution of herbicide resistance is context-dependent and that secondary stressors like insecticide can alter the evolutionary trajectories of plant defense.

Parthenogenesis is relatively rare and often regarded as an evolutionary dead end. Despite this, certain parthenogenetic animal species have endured for millions of years, but it is unclear what enables the persistence of some parthenogenetic lineages. Transitions from sexual to parthenogenetic reproduction can occur through different evolutionary processes that give rise to diverse cytological reproductive mechanisms. These mechanisms are likely to influence genetic diversity, especially in the early stages after the transition to parthenogenesis and may thus affect lineage persistence. To understand such evolutionary transitions, we used experimental crosses to investigate the mechanism of parthenogenesis and the immediate genetic consequences of switching from sexual to parthenogenetic reproduction in the facultatively parthenogenetic phasmid Megacrania batesii. We obtained DNA sequence data from multiple lineages propagated over three generations via sex, parthenogenesis, or transitions between reproductive modes. We quantified heterozygosity and within-family genetic variation and compared the genetic patterns with predictions for known mechanisms of parthenogenesis. We found that a single generation of parthenogenesis typically resulted in (near-)complete loss of heterozygosity and an absence of within-family genetic variation, consistent with automixis with gamete duplication or terminal fusion and little/no recombination. However, we also found evidence of variation in the mechanism of parthenogenesis among lineages and even within the same individual, associated with drastic differences in the amount of heterozygosity and within-family genetic variation maintained across generations. Our findings show that considerable variation in parthenogenetic mechanisms can exist within populations and suggest that such variation could influence the persistence and evolution of parthenogenetic lineages.

Animal mating systems are hugely diverse, ranging from species where mating is essentially random to those exhibiting complex systems of mate choice by one or both sexes. While polygyny and mate choice are known to alter adaptation and persistence in a changing environment, there has been little exploration of the ways that adaptation and evolutionary rescue are modulated by other types of mating systems. We developed an individual-based model that allows random mating, female-only choice, and mutual mate choice to be compared between monogamous and polygynous frameworks and used it to explore how mating systems influence adaptive response, loss of heterozygosity, and extinction risk under worsening environmental conditions. We find that mating systems interact with population size in determining extinction risk: mate choice under polygyny lowers effective population size, small polygynous populations with either mutual or female-only mate choice lose heterozygosity quickly and so face higher extinction risks than randomly mating populations. However, in larger populations where inbreeding and genetic drift are less important, mate-choice-based polygynous systems enhance evolutionary rescue by allowing better-adapted males to dominate reproduction, accelerating adaptation and increasing resilience to environmental change. Among polygynous systems, female-only choice leads to slower loss of heterozygosity and facilitates population resilience better than mutual mate choice. These findings demonstrate that mating systems can critically shape a populations ability to adapt to environmental change and alter extinction risks, emphasizing the need to consider mating systems in designing effective conservation strategies. Significance StatementEnvironmental change threatens species survival, and sexual selection can have profound modulating processes that determine extinction risk. Sexual selection operates in a variety of mating systems, and the role of this diversity is often overlooked. Using individual-based simulations, we show that mating systems with mate choice boost evolutionary rescue in larger populations via "good genes," while in small populations, it has the opposite effect by elevating the loss of heterozygosity. These results have critical implications for conservation biology. Conservation strategies should consider mating system characteristics when assessing species vulnerability and planning management efforts to support evolutionary resilience and long-term population persistence.

Phenotypic plasticity allows plants to rapidly respond to changing environments without the need for evolutionary change or migration. While selection can create variation in plasticity across natural populations, these responses are not adaptive in all environments. To predict whether plasticity will be adaptive requires evaluation of its fitness effects across a range of environments, including novel ones. Here, we test how traits and their plasticity vary for genotypes collected across a natural hybrid zone between two tree species with contrasting climatic niches. Fast-growing Populus trichocarpa inhabits maritime environments with relatively warm and stable temperatures, while P. balsamifera inhabits continental environments with cold winters and large temperature variance throughout the year. We planted 44 clonally replicated genotypes into thirteen common gardens and measured vegetative phenology, leaf morphology, stomata morphology and conductance, and photochemistry. Overall, genotypes from colder, more continental environments exhibited higher plasticity. P. balsamifera ancestry was associated with increased plasticity in timing of fall phenology, stomatal conductance, and leaf mass per unit area. We assessed the effects of trait plasticity on fitness estimated as yearly growth across common gardens and found that the plasticity-fitness relationship was often garden-specific, indicating that the planting environment did not consistently mediate plasticity-fitness relationships. When the effects of trait plasticity on growth varied by garden temperature, higher plasticity generally had neutral or negative associations with growth in warmer environments. These results suggest that elevated plasticity evolved in a P. balsamifera genomic background as part of a climate generalist strategy to seasonal temperature variability, but that there is a trade-off between plasticity and growth in warmer environments. Consequently, less-plastic but warm-adapted P. trichocarpa genotypes are likely to have a fitness advantage under warming climates. These results demonstrate that plasticity may sometimes be maladaptive and will not be universally beneficial in a warming world.

Premise of studyUnder increasingly frequent pollinator-limited environments, plants need to rely on modes of reproductive assurance such as selfing and cloning. However, few studies investigate the interplay between selfing and cloning in plants that can do both. Here, we explore mechanisms determining the relative expression of selfing and cloning throughout the European distribution of the wild woodland strawberry (Fragaria vesca) under a pollinator-free environment. MethodsWe established an outdoor common garden with 121 woodland strawberry genotypes from across Europe and excluded them from pollinators. For each genotype, we recorded reproductive traits and performed hand-pollination treatments. Key ResultsWe found a weak trade-off between cloning and selfing, driven by increased seed and fruit provisioning rather than flower production. The capacity to autonomously self-fertilize was determined by the lateral proximity of the anthers to the pistils (lateral herkogamy), but not by early inbreeding depression. Genotypes sampled at lower latitudes and altitudes were better at self-fertilizing and had smaller petals. The propensity to clone increased towards the east, where genotypes also had smaller petals, particularly at higher latitudes. ConclusionAt the species level, we detected a trade-off between the propensity for clonal reproduction and the capacity for self-fertilization. At a continental scale, the capacity to self-fertilize varied along a north-south gradient, whereas clonal propensity varied along an east-west gradient. Our results suggest that these two modes of reproductive assurance may compensate for reduced pollinator attractiveness (smaller petals) in regions where each mode is most strongly expressed.

Biological diversity driven by endosymbiosis arises from the intertwined evolution of microbes and their hosts. Each partner affects the fitness and therefore the evolution of the other. Here, we tested a further question: does the history of symbiosis affect evolution even after the partnership is dissolved? We analyzed phenotypic data from experimentally evolved strains of Dictyostelium discoideum hosts, each of which had had its symbiont removed, to study how their traits evolved. We found that host trait evolution was affected by the prior history of infection, specifically by which of three Paraburkolderia bacterial symbionts had been removed. Thus, symbionts affect not only current evolution but also generate path dependence that affects the subsequent evolutionary trajectories even after the symbionts are lost. Impact statementThe evolution of partner dependence in host-microbial symbioses has fundamentally shaped biological diversity and ecosystem function. To examine variation in symbiont dependence in the social amoeba, we compared how different strains of Dictyostelium discoideum respond evolutionarily after the loss of their bacterial symbionts. We analyzed phenotypic data from experimentally evolved strains and found that the absence of different symbiont species leads to distinct changes in the subsequent evolution of key traits like cell proliferation, slug migration, and spore production. This research expands our current understanding of microbial symbiosis by revealing that symbiont species may impact the evolution of their hosts even after the symbiont is gone. Data summaryWe used phenotypic traits data from our previous experimental-evolution dataset from the open-access repository Dryad (https://doi.org/10.5061/dryad.kkwh70s97). Scripts for the statistical analyses are available in a GitHub repository (https://github.com/jahanisrat/SymbiontLoss). The accompanying R project includes code to reproduce the graphs in the results section.

According to sexual selection theory, males should benefit more from mating with multiple partners than females do, as male investment into offspring production is typically lower. For females, empirical evidence indeed often shows diminishing returns or even costs of mating multiply. For males, the assumption often seems to be "the more, the better" - i.e., a steady increase of male reproductive success with mate number - but experimental tests of it are rare. Here we used a laboratory experiment with Trinidadian guppies (Poecilia reticulata), known for being promiscuous, to assess how pairing males weekly with 4 vs. 7 females affects both sexes reproductive performance (n = 32 polygynous males and 170 monogamous females). Increased polygyny delayed females reproductive onset by 9% and tripled their risk of reproductive failure. High-polygyny males fathered offspring with 49% more females and had 73% higher daily reproductive output. Yet, they needed 19% longer to initiate pregnancy, and only accumulated more offspring than low-polygyny males after two months. This study suggests that male mating performance is not unlimited. Especially when high extrinsic mortality selects for fast reproduction, less polygyny might be advantageous, and the strength of sexual selection perhaps more similar between the sexes than often assumed.

Hybridisation outcomes often vary across space and time, yet the relative roles of demographic history and genomic architecture in shaping introgression remain unclear. Here, we investigate three replicated hybrid zones between the damselflies Ischnura elegans and Ischnura graellsii across Spain to test whether genomic introgression patterns are repeatable across independently formed zones. Using genome-wide data, we combined demographic modelling, genomic cline, and functional annotation of introgressed loci. Demographic inference supported three independent secondary contact events of different ages: The South-east zone forming first ([~]207 years ago), followed by the North-west ([~]73.5 years) and North-central ([~]33 years) hybrid zones. Despite similar cline steepness across autosomes, asymmetric gene flow from I. graellsii into I. elegans was observed, with a low overlap of introgressed loci between zones. These loci were mainly associated with broad regulatory and transport-related functions in both hybrid zones, indicating repeatability at the level of gene function rather than gene identity. In contrast, the X chromosome showed steeper clines, suggesting strong intrinsic genomic constraints. Together, demographic history explains geographic heterogeneity in introgression, whereas chromosome architecture imposes consistent constraints. These findings highlight how replicated hybrid zones can disentangle contingent versus repeatable genomic responses during early stages of speciation with gene flow.

De novo gene emergence from non-coding sequences is increasingly recognized as an important evolutionary mechanism, yet the functional potential of random sequences remains debated. Previous experiments suggested that expression of random sequence clones in Escherichia coli can enhance growth of the cells bearing them, i.e. they provide a fitness advantage. However, these findings have been questioned, regarding potential confounding effects of the clone mixtures and a possibly negatively acting peptide expressed from the cloning vector. Here we performed controlled competitive growth assays using a defined subset of 64 random sequence clones representing a spectrum of fitness effects. Experiments across multiple conditions, including two different growth cycle durations, induction states, and replicate sets, showed high technical reproducibility and consistent clone-specific growth trajectories for the majority of the clones, but for some also influences of genomic background and experimental conditions. While vector-derived constructs that inhibit the vector-coded peptide expression showed the same fitness improvements relative to the parental vector that were previously shown, several random sequence clones exhibited higher positive selection coefficients under conditions of exponential growth. These effects persisted even when negative clones were excluded, indicating that they are not driven by competition dynamics with negative clones. Our results demonstrate that positive growth effects of random sequence clones cannot be explained by clone mixture and vector artifacts alone. Instead, a subset of random sequences confers genuine fitness advantages comparable to beneficial mutations observed in experimental evolution studies. These findings provide strong experimental support for the capacity of random sequences to generate adaptive functions and underscore their role in de novo gene evolution. Significance statementThis study provides robust experimental evidence that a subset of random DNA sequences can confer genuine fitness advantages in Escherichia coli, independent of previously proposed artifacts such as vector effects or clone competition. Based on controlled competitive assays across multiple conditions, the results show that these adaptive effects are reproducible and comparable to beneficial mutations observed in experimental evolution. These findings strengthen the case that random sequences can serve as a meaningful source of functional innovation, supporting their role in de novo gene evolution.

Hybridization is a powerful force shaping the evolutionary trajectories of species, yet its outcomes are highly variable both across taxa and within a pair of species. In this study, we examine the processes shaping variation in the extent of hybrid ancestry, both among populations and across the genome. We use low-coverage sequencing data to infer local ancestry across the genome for 782 individuals from multiple populations across two geographic regions within the broadly overlapping range of Mimulus guttatus and Mimulus nasutus. We find that the extent of hybrid ancestry is variable across populations, supporting disparate historical patterns of hybridization. However, genomic patterns of hybrid ancestry are correlated across groups, indicating they are shaped by parallel processes. Correlations are highest in geographically proximal populations, including between sympatric and allopatric locations, providing evidence that introgression is not locally constrained but spreads via migration across the landscape. We find that features of the genome are predictive of hybrid ancestry and its correlations among populations. However, contrary to findings in some other species, these patterns are likely not driven by simple linked selection against hybrid ancestry. Genomic outliers for high hybrid ancestry are often shared among populations, suggesting a role for parallel positive selection on ancestry. However, known loci associated with reproductive isolation are poor predictors of ancestry variation across populations, indicating that selection acting in natural hybrid populations is highly polygenic and that the underlying genetic architecture varies across space. Overall, this study demonstrates how ecological, demographic, and genomic features all interact to shape the outcomes of hybridization.

Predator-prey interactions are key drivers of behavioural and life-history evolution, yet their mechanisms remain difficult to study in natural contexts. The nematode Pristionchus pacificus is a model predator, but most studies exploring its behaviours use Caenorhabditis elegans as prey, a species that it likely only rarely encountered in nature. Here, we examine predation within nematode communities associated with beetle carcasses, the native necromenic habitat of P. pacificus. We identify Oscheius myriophilus as a cohabiting species, likely representing natural prey. Using predatory assays, automated tracking, and machine-learning-based behavioural analysis, we show that P. pacificus actively kills and consumes O. myriophilus. Strikingly, predation rates are lower than those observed for C. elegans, suggesting partial resistance or reciprocal adaptation in O. myriophilus. Consistent with this, O. myriophilus exhibits a mixed reproductive strategy, with early oviposition followed by ovoviviparity and matricide. As later developmental stages are more resistant to predation, internal hatching may protect offspring while providing maternal resources for development. These findings establish these nematodes as a tractable model for investigating predator-prey interactions and their evolutionary consequences, highlighting how behavioural strategies and life-history traits can co-evolve in natural communities.

Restoration and management of natural populations often assume that local genotypes are best suited for transplantation to their local environment. Prioritizing a single local genotype, however, contrasts with the framework of maximizing intraspecific diversity to increase population resilience to environmental change. Local populations may also become maladapted to a rapidly changing environment, motivating alternative frameworks that instead minimize environmental distance between source and transplantation sites. Here, we tested the predictive power of the local is best, maximize intraspecific diversity, and minimize environmental distance frameworks on the survival and growth of Eastern oyster (Crassostrea virginica) genotypes in field common gardens that differed in salinity and disease pressure. Although a genome scan revealed patterns of adaptation to disease, heat stress, and salinity among source populations, we did not find strong support for the local is best framework: geographically distant southern genotypes performed comparably to local selection lines and a local wild population. Higher genetic diversity within monocultures was associated with higher survival, yet highly diverse polycultures survived at lower rates than the best-performing monocultures, providing mixed support for the maximize intraspecific diversity framework. Temperature and salinity of the environments-of-origin of parents predicted the survival of their offspring in common gardens, but the relationship between survival and environmental distance was context-dependent, leading to mixed support for the minimize environmental distance framework. Together, these results demonstrate that no single framework reliably predicted transplantation success, suggesting that effective management strategies may need to integrate genomic and environmental lines of evidence to guide genotype selection.

Alleles with opposing effects on fitness characters are said to exhibit selectional antagonistic pleiotropy (broadly construed so that effects are not necessarily confined to the same individual). A number of theoretical investigations considered the case where a pair of alleles at a locus influences two fitness components and derived the conditions giving rise to stable polymorphism under various assumptions about the mode of trait-interaction. Strikingly, many of these analyses concluded that the potential for maintaining polymorphism is strongly constrained by the joint influence of two factors: (1) the prevalence of weak selection coefficients over coefficients of large magnitude, and (2) the absence of beneficial dominance reversals (where the deleterious effects of each allele are partially or completely masked in the heterozygous genotype). Consequently, the conclusion that selective polymorphism is unlikely to be maintained by intralocus mechanisms of antagonistic pleiotropy has achieved widespread acceptance. Here we argue that such conclusions do not apply to any of the following models of antagonism: (i) additive trait-interaction, (ii) multiplicative trait-interaction, (iii) bivoltine selection, (iv) soft selection, (v) hard selection, and (vi) sexual antagonism. We demonstrate that the parameter space giving rise to stable allelic variation is quite large throughout, and moreover, the plenitude of suitable parameters neither depends on the strength of selection nor requires dominance reversal. Dominance coefficients associated with stringent conditions for stable polymorphism are shown to be atypical as compared to all feasible parameters, and best regarded as an outcome of adherence to a special relation: dominance with a constant magnitude and direction, which includes the case of additive allelic effects at a locus. Properties of single-locus equilibria (heterozygosity, allele frequency differentiation) are investigated, as well as the contribution of dominance schemes to the genetic variance in fitness characters in populations at multilocus linkage equilibrium. Author summaryAllelic variants at a locus with opposing effects on multiple fitness components (antagonistic fitness pleiotropy) have long been appreciated as a possible source of balancing selection. The prevalence of polymorphism owing to this form of natural selection, however, has been doubted on theoretical grounds due to the fact that standard assumptions of genetic models (namely, constant magnitudes for the dominance coefficients) are hardly conducive to the maintenance of polymorphism. The major exception to this conclusion lies with schemes that exhibit dominance reversal (where the direction of dominance for antagonistic alleles flips across fitness components). Here we conduct a geometric analysis of the space of polymorphism-promoting dominance parameters and conclude that the conditions for maintaining balanced alleles is unrestrictive, with non-reversals playing an underappreciated role.

Repeated divergence across contrasting habitats is widely used to infer natural selection and local adaptation. However, such inferences remain inherently correlative and capture only adaptation shared within habitat types, thereby missing site-specific adaptation among populations from the same habitat type. Field transplant experiments test adaptation more directly by measuring fitness in nature, but they are typically limited to pairwise reciprocal exchanges between populations and therefore cannot separate the contributions of shared habitat-level and site-specific adaptation to fitness. Here, we overcome these limitations by extending the typical transplant framework to include multiple populations transplanted both within and across habitat types. We apply this framework to lake-stream stickleback, a classic system for studying local adaptation via repeated divergence. Specifically, we transplanted laboratory-reared fish from a panmictic lake population and four independently evolving stream populations into one lake and two stream sites. Stream fish outperformed lake fish in streams and vice versa, providing evidence for adaptive lake-stream divergence. Strikingly, local stream fish also outperformed foreign stream fish at both stream sites. This site-specific advantage was twice as large as the advantage of foreign stream fish over lake fish, which reflects the fitness benefit of shared stream adaptation. These results show that in this system, the majority of fitness-relevant evolutionary variation is site-specific and therefore missed by approaches that rely on repeated divergence to infer adaptation. More broadly, this underscores the importance of ecological scale for understanding adaptation and evolutionary predictability.

Population genetic theory predicts that natural selection will be more efficient in large than small populations because genetic drift reduces the efficiency of selection in small populations. Small populations adapting to new environments can also be expected to evolve higher recombination rates to facilitate adaptation as well as to dissociate and purge harmful mutations. We tested these hypotheses (1) by investigating differences in the strength of association between nucleotide diversity ({pi}) and recombination rate across the genomes of nine-spined sticklebacks (Pungitius pungitius) from four small freshwater (mean Ne {approx} 2 578) and four large marine (mean Ne = 86 742) populations, as well as (2) by comparing recombination rates between small and large populations using population specific linkage maps. We found the predicted positive correlation of{pi} with recombination rate from all but the smallest freshwater populations, suggesting prevalent linked selection even after accounting for variation in GC/CpG content, and gene density. Mean recombination rates did not differ between freshwater and marine populations, except that the smallest Ne freshwater population exhibited significantly elevated recombination rate. GWAS analyses suggested a polygenic basis for recombination rates. These results suggest an important role for linked selection in reducing{pi} in low recombination regions especially in large populations. Moreover, as predicted by theory, at least one of the small freshwater populations appears to have evolved a higher recombination rate than its marine ancestors.

When invasive populations establish in regions far from their origin, they risk accumulating harmful mutations (genetic load) that limit population viability and subsequent spread. This may be exacerbated by the multiple, sequential bottlenecks experienced when invasions stem from a bridgehead population. However, populations may be able to purge genetic load when they can outbreed with other lineages from subsequent invasions. Here, we analyse global invasions of a species complex of persistently inbreeding ambrosia beetles, using genomic data (N=247) from invasive populations in Africa, North America and Australia, and from native populations in Asia. We focus particularly on one species of this complex (Euwallacea fornicatus) which poses a catastrophic threat to tree species worldwide and is rapidly expanding its global range. We uncover a single lineage of this species across South Africa, California and Western Australia, derived from an invasive bridgehead and containing almost no nuclear genetic variation. In South Africa we identify a second lineage that has repeatedly hybridised with the first lineage. Genetic patterns in the native range indicate that such opportunistic outbreeding may be common. Although purifying selection was evident in all lineages, native populations had fewer missense mutations than invasive populations, suggesting that opportunistic outbreeding may help purge fixed deleterious mutations when local lineage diversity is high. These findings show how inbreeding depression can affect populations even where inbreeding is common, and they highlight the biosecurity threat posed by subsequent gene flow into invasive populations.

A central but poorly resolved question regards how genome architecture shapes the selection response and repeatability of polygenic adaptation. We addressed this question using Evolve-and-Resequence experiments under rapid salinity decline in two sibling species (clades) of the invasive copepod Eurytemora affinis complex that differ strikingly in chromosome number (15 versus 4). The 4-chromosome genome arose from chromosomal fusions of the ancestral 15-chromosome genome, bringing together coadapted alleles at fusion sites. Across 10-20 generations of selection, both clades adapted to low salinity but followed divergent evolutionary trajectories. The selection lines of the 15-chromosome clade exhibited highly parallel genomic responses, whereas the 4-chromosome clade lines showed delayed and less repeatable responses. Forward genetic simulations revealed that strong synergistic epistasis among beneficial alleles best explained elevated parallelism in the 15-chromosome clade. Additional simulations varying chromosome number and epistasis revealed that strong positive epistasis, combined with high chromosome numbers, enhances parallelism by enabling recombination to assemble coadapted allelic combinations. In contrast, the high starting frequency of beneficial alleles in the 4-chromosome clade lines indicated selection on standing variation, likely acting on alternative linked haplotypes. These findings demonstrate that genome architecture and gene-gene interactions jointly determine the dynamics and predictability of polygenic adaptation.

Transitions from sexual to asexual reproduction are well-documented across different taxa. However, despite extensive efforts, the regulatory changes underlying the emergence of asexuality remain largely undiscovered in the majority of species studied. Artemia brine shrimp have multiple closely related sexual and obligate parthenogenetic lineages, making them a promising model for addressing this question. While earlier work suggested that asexuals use a modified meiosis, and inferred a likely role for the Z-chromosome in its transmission, no master regulator or genetic changes have been put forward as the root causes for the shift. Here, we generate single-nucleus RNAseq data of the female reproductive system of individuals from the Aibi lake population of Artemia parthenogenetica and its closely related obligate sexual species Artemia sp. Kazakhstan. We identify the germline cell clusters in the female reproductive system and perform differential expression analysis to infer substantial transcriptional differences at genes putatively involved in cell cycle and oocyte development between the meiotic cells of the two species. Additionally, we use whole-genome sequencing of 32 individuals from two backcrossing experiments to narrow down the genomic regions associated with the transmission of asexuality to an 8 megabase region of the Z chromosome. Within the identified regions, two adjacent genes with known functions in oogenesis, ITPR and USP8, show differential expression and genetic differentiation between sexuals and asexuals, making them promising candidate drivers of asexuality in this species. Significance statementWhile most animals reproduce sexually, many do not, and why and how these shifts occur remains an open question. This paper presents a systematic investigation of the molecular changes that underlie the transition from sexual to asexual reproduction in brine shrimp. We combine multiple computational and experimental approaches to look for differences between close sexual and asexual lineages. We find that a subset of meiotic germ cells is regulated differently in the two, and that two important oogenesis genes are the likely drivers of asexuality. This work is unique in providing an in-depth characterization of the combined genetic and regulatory changes underlying this key transition in reproductive modes.

Population genetic models excel at identifying the conditions for polymorphisms based on balancing selection but typically disregard the ecological processes that yield particular values of selection coefficients. We model a system that combines antagonistic pleiotropy, dominance reversal and heterozygote advantage: the wood tiger moth Arctia plantaginis, where alternative haplotypes at a major-effect locus determine male hindwing coloration. Yellow offers better protection against predators, while white is often associated with better mating success. The effects of mortality and reproductive success overlap in time because protandrous males can mate as long as they are alive, but they need to avoid predation for several days before the bulk of females emerge. We show that protandry aids polymorphism maintenance whenever the second-fittest genotype (after the heterozygote) is the poorly surviving but mating advantaged homozygote, while increased protandry harms polymorphism when the second-best fitness is that of the survival advantaged morph. Ecologically plausible protandry times predict that dominance reversal does not have to be strong for polymorphism to be maintained. Our study highlights the importance of timing traits in maintaining polymorphisms in Lepidoptera and showcases the benefits of deriving fitness explicitly in place of abstract selection coefficients that lack temporal components within the life cycle.