Evolution Letters

Populations often persist in novel environments despite predictions that adaptive capacity to such conditions should be limited by a lack of genetic variation. A leading hypothesis is that genetic variation for adapting to novel environments is maintained but remains hidden under native conditions. However, direct evidence for the mechanisms that maintain this adaptive potential in natural populations is scarce. Here, we integrate data from four large-scale field experiments to test whether variation in selection across life history and environments, together with genetic architecture, maintains genetic variation important for adapting to novel environments. Using a quantitative genetic breeding design, we generated families of the Sicilian daisy, Senecio chrysanthemifolius (Asteraceae), and planted seeds and cuttings across native and novel elevations on Mount Etna. We tracked fitness across elevations, life stages, seasons and generations. Genotypes with higher survival and flowering success at the novel elevation increased adaptive potential, but were only weakly selected against in the native environment where they had slightly lower fitness at a later life-history stage. A negative genetic correlation in seedling survival across seasons indicated that different genotypes were favoured across temporal variation in native environments. Crosses between genotypes with low and high fitness in the novel environment revealed that genotypes that increased adaptive potential had heritable effects on plasticity and fitness across generations, but were recessive and therefore largely hidden in heterozygotes. Together, these results provide rare field-based evidence that weak selection in native environments, temporal variation in selection and dominance effects act together to maintain cryptic adaptive potential in natural populations.

Transgenerational plasticity (TGP)- when parental environments influence offspring phenotypes - is ubiquitous across taxonomic groups and can have benefits for offspring beyond what is possible with developmental plasticity, particularly when selective pressures are high early in life. However, patterns of TGP vary widely across populations and species, and the evolutionary processes shaping this variation remain poorly understood. Here, we tested whether repeated evolutionary transitions result in parallel or population-specific evolutionary divergence in TGP relative to ancestral conditions. We examined sperm-mediated paternal effects across two ancestral marine and three derived freshwater populations of threespined stickleback fish (Gasterosteus aculeatus). We exposed fathers to dragonfly larvae (endemic to freshwater) or sculpin (endemic to all populations) predators and measured both paternal response to predators as well as antipredator behavior and growth in larval offspring. Fathers behaviorally responded to the presence of sculpin predators, but not dragonfly larvae. However, we found strong paternal effects in response to both predators in all populations. Further, the magnitude of TGP did not differ between marine and freshwater populations, suggesting that TGP does not become genetically accommodated as marine populations move into freshwater habitats. We found some evidence consistent with parallelism in both within and trans-generational plasticity: 1) personal exposure of larval stickleback to dragonfly larvae elicited strong antipredator responses in freshwater populations that were absent in marine populations, and 2) paternal predation exposure consistently increased offspring growth in marine populations while slowing growth in freshwater populations. In contrast, paternal effects altered offspring behavior in population-specific ways, with strong sex-specific effects of paternal exposure emerging in response to endemic predators. Adaptive evolution is a two-step process, in which heritable genotypic and phenotypic variation must first be present and then selected on. Therefore, high population-level variation in TGP suggests the capacity for rapid evolution of parental effects, while signatures of parallelism and sex-specific patterns suggest that TGP may evolve in targeted ways in response to ecological stressors.

The size of an epidemic can influence the strength of selection acting on hosts and parasites, but whether epidemic size consistently shapes host-parasite (co)-evolution remains unclear. I conducted a meta-analysis of studies that simultaneously quantified epidemic size and evolutionary change in hosts, parasites or their interactions, synthesising 123 effect sizes from 11 studies. I tested whether epidemic size was associated with four components of evolutionary change: host evolution, parasite evolution, non-additive host-parasite coevolution and net coevolution. Larger epidemics were associated with greater host evolutionary change in invertebrates, whereas the relationship was positive in plants and negative but non-significant in bacteria. Parasite evolution, non-additive coevolution and net coevolution were not detectably associated with epidemic size, although parasite infectivity showed a relatively consistent increase across studies. These results provide limited evidence for a general relationship between epidemic size and host-parasite (co)-evolution and instead suggest that evolutionary responses depend on the host-parasite system and broader ecological and temporal context. Interpretation is constrained by the small and taxonomically biased evidence base, particularly the strong representation of Daphnia, and by substantial heterogeneity in how epidemic size and evolutionary change were measured and defined. More studies across diverse host-parasite systems are required that track both evolutionary change and disease prevalence through time. This work also provides an empirical basis for incorporating coevolutionary feedbacks into quantitative epidemiological models.

Demographic history can profoundly shape genomic variation by altering levels of inbreeding, the strength of genetic drift, and the efficacy of purifying selection, thereby influencing both the accumulation and expression of deleterious variation. Yet the extent to which these genomic consequences translate into organismal performance remains poorly understood. Here, we investigated how contrasting demographic histories shape genomic diversity, inbreeding, genetic load, and performance across mainland and insular populations of the Italian wall lizard, Podarcis siculus. Using whole-genome sequence data from 263 wild-caught individuals and field-based performance measurements from 134 lizards, we characterised population structure and demographic history, quantified genomic diversity, runs of homozygosity, and deleterious variation, and tested associations between genomic inbreeding and performance traits. Island populations showed reduced genetic diversity, increased autozygosity, and elevated genetic load relative to mainland populations, consistent with stronger genetic drift and reduced efficacy of purifying selection. Patterns of deleterious variation were consistent with purging of strongly, but not mildly, deleterious variants. Greater genomic autozygosity was associated with reduced bite force in island lizards, a pattern consistent with inbreeding depression, whereas sprint speed, sperm quality, immunocompetence, and spatial cognition showed no significant association with inbreeding. Genome-wide mapping of runs of homozygosity further identified multiple genomic regions associated with reduced bite performance. Together, these results show how demographic history shapes genomic diversity, homozygosity, and deleterious variation in wild vertebrate populations, while revealing that phenotypic consequences can be trait-specific, a pattern that may reflect differences in genetic architecture and the extent of environmental influence on trait variation.

Global warming will impact natural selection on plant traits and their plasticity by influencing phenotypes, biotic interactions, and fitness. Because warming affects biotic interactions, community composition may influence how warming affects selection on plants, but this is little studied. We grew full-sibling pairs of Brassica rapa plants in an ambient and hot temperature environment and exposed them to visitation by a pollinator (Bombus terrestris), a pollinating herbivore (Pieris rapae), or their combination. We recorded plant phenotypes, insect visitation, herbivory, and plant fitness. We used these to calculated phenotypic selection on plant traits and their plasticity, including additive and nonadditive effects. Elevated temperature changed selection on traits related to pollinator attraction, such as flower number, nectar production, and floral scent emission. We found both positive and negative selection on temperature-mediated trait plasticity depending on the biotic treatment. Elevated temperature changed patterns of additive and non-additive selection on a variety of traits including flower morphology and scent. This study shows that elevated temperatures can reshape patterns of phenotypic selection, including nonadditive effects, and plastic trait expression. Effects of elevated temperature on phenotypic selection depended on the biotic interactors, highlighting the importance of community context for the effects of warming on natural selection.

Eco-evolutionary responses to long-term environmental deteriorations will fundamentally depend on interactions between plasticity and evolution of life-history traits that shape population dynamics. Counter-intuitive evolutionary and (meta)population dynamics could arise when different components of individual-specific and/or shared site-specific developmental and labile plasticity affect traits with intrinsically non-linear genotype-environment-phenotype relationships, especially given density-dependent fitness outcomes. Frequency-dependent evolutionary responses could then emerge, but resulting eco-evolutionary dynamics and outcomes have rarely been considered. By modelling a partially-migratory metapopulation encompassing facultative seasonal migration versus residence formulated as a quantitative genetic threshold trait, we show how different forms of plasticity in liability to migrate interact with spatio-seasonal metapopulation dynamics to generate divergent eco-evolutionary responses to spatially restricted environmental deterioration. Temporary and permanent individual-specific environmental effects induced faster evolutionary recovery than might simply be expected, by revealing cryptic genetic variation and allowing adaptive phenotypic changes through repeated episodes of selective disappearance. Conversely, shared subpopulation-specific environmental effects caused among-year variation in phenotype frequencies, impeding evolutionary responses to the extent that migratory metapopulation connectivity was ultimately eradicated. We thereby reveal key principles of how structurally different forms of plasticity in a dichotomous quantitative genetic trait can induce complex eco-evolutionary dynamics, culminating in differing degrees of evolutionary rescue versus constraint.

How natural populations maintain genetic variation for fitness remains a central problem in evolutionary biology. Theory predicts that opposing selective pressures across environments can preserve fitness-associated polymorphism, but how interactions among species contribute to this process remains poorly understood. Here we show that host diversity preserves standing genetic variation within sexual populations of the leafmining fly Scaptomyza flava. We evolved twelve populations for ten generations on either of two naturally co-occurring host plants or on both, pooling survivors from the two hosts before mating. Single-host populations evolved reciprocal fitness trade-offs, whereas two-host populations maintained relatively even performance across hosts. Whole-genome time series dynamics identified a linked region in which alleles increased on one host and decreased on the other, while showing little net change under two-host conditions. Wild flies reared from the two hosts showed corresponding allele-frequency differences within this region. Across the genome, two-host populations retained more rare variants than populations evolving on either host alone. These findings show that selection imposed by different host species in sympatry can maintain standing genetic diversity within an herbivore population.

The additive genetic variances and covariances of traits, collected in the G-matrix, summarise heritable variation within populations and are commonly used to predict the rate and direction of short-term multivariate evolution. These (co)variances are shaped by pleiotropy and genetic linkage, two features often associated with supergenes formed by chromosomal inversions. Yet how supergene evolution affects the structure and temporal stability of the G-matrix remains unclear. Here, we use mathematical analysis and individual-based simulations to investigate the evolution and genetic consequences of inversions capturing multiple pleiotropic loci underlying two traits subject to disruptive and correlational selection (selection favouring particular combinations of trait values). We show that inversions evolve under disruptive selection and are maintained by balancing selection because they preserve associations among alleles that together generate discrete phenotypic morphs. The genetic architecture reflects how selection acts on the traits: selection favouring diversification along a joint trait combination generally produces a single multi-trait supergene, whereas selection favouring independent diversification of each trait produces multiple independently segregating inversions. By suppressing recombination, these inversions increase additive genetic variance and narrow-sense heritability, and stabilise the overall amount of additive genetic variation through time. When dominance is allowed to evolve, dominance relationships become coordinated across linked loci within supergenes, although most genetic variance remains additive at the population level. Together, these results link the form of multivariate selection to the evolution of supergenes and to their consequences for the structure and temporal stability of the G-matrix.

Co-occurring species often face similar selective environments, although adaptive responses to these environments are generally assumed to be species-specific, particularly in complex landscapes where selective pressures are likely to be multi-dimensional. We test this assumption by contrasting genotype-environment associations (GEAs) among a range of co-occurring but unrelated plants with different life histories from an isolated, mountainous national park in south-eastern Australia. Analyses were performed using single nucleotide polymorphism (SNP) loci derived from reduced genome representation sequencing to investigate genomic associations with spatial and environmental drivers across unrelated plant species within the same heterogeneous landscape. Several species showed GEAs that aligned with similar environmental gradients, particularly edaphic features, suggesting that similar selective pressures can shape genomic responses across taxa. Other species exhibited distinct spatial and environmental associations, highlighting idiosyncratic outcomes. Notably, GEAs were detected at fine spatial scales despite generally low levels of genome-wide divergence, suggesting adaptive variants can persist in the face of gene flow under strong selective pressure. This study highlights how community-level genomic diversity is shaped by common environmental processes, with implications for biodiversity management in rapidly changing environments, where diverse ecosystem-level responses to selection may underpin resilience.

Species interactions shape ecological dynamics, but adaptation to one interaction can trade off with others. Experiments that measure such evolved fitness changes across multiple interactions remain rare. We used experimental evolution to test whether recent selection under one ecological interaction changes fitness under other interactions in a fly-parasitoid system. We evolved a genetically diverse Drosophila melanogaster population for 15-17 generations under three regimes: benign conditions (control), high intraspecific competition, and infection by the parasitoid wasp Leptopilina boulardi. We then measured fly fitness (egg-to-adult survival and subsequent reproduction) under benign conditions, high intraspecific competition, and infection by three other parasitoid species and an additional conspecific L. boulardi strain. Selection history strongly influenced fitness across interactions. Populations maintained under high larval density showed reduced survival under infection by L. boulardi and L. victoriae, indicating a trade-off between past selection for competition and defence against some parasitoids. Populations evolved under parasitoid infection by L. boulardi showed increased resistance to a conspecific strain but reduced fitness when infected by another species, L. heterotoma. Our results show that rapid evolution in response to a single interaction can reshape multiple ecological interactions through fitness trade-offs, highlighting how recent evolutionary history may influence community dynamics and invasion susceptibility.

Understanding the role of sexual selection in shaping evolutionary trajectories is a key goal of biology, and thus developing a genomic measure of sexual selection strength is desirable. In systems with ZW sex determination, the ratio of nucleotide diversity ({pi}) on the male-biased Z chromosome to that on the autosomes (the Z:A ratio) is expected to decline as male effective population size decreases under strong sexual selection, offering one such measure. However, non-equilibrium processes other than sexual selection (e.g., hybridization, changes in population size) can influence levels of Z-linked diversity relative to the rest of the genome, complicating interpretation of this metric and necessitating a systematic evaluation of how Z:A ratios vary across known demographic and selective circumstances. We leveraged longitudinal sampling over a [~]25-year period in Manacus manakin populations in western Panama, spanning a mainland transect (including M. candei, M. vitellinus, and their hybrid zone) and insular populations of the Bocas del Toro Archipelago. On the mainland, Z:A ratios were temporally stable within populations, but varied across populations: (1) Z:A ratios were lower in M. vitellinus than M. candei, likely due to stronger sexual selection in the former; and (2) Z:A ratios increased at the hybrid zone center, likely due to fast-Z effects in parentals inflating Z:A ratios in recent hybrids. Island populations exhibited significantly lower Z:A ratios than mainland populations, consistent with theoretical expectations of Z:A reductions following population contractions as the islands became isolated. Insular Z:A ratios increased with proximity to other landmasses, suggesting gene flow mitigates these effects in this system. While the Z:A ratio behaved predictably in relation to known non-equilibrium processes, our results demonstrate the potentially strong effects of demographic history and admixture on Z-linked diversity, which should be considered in studies aiming to use the Z:A ratio as a measure of sexual selection.

The faster-X effect predicts that X chromosomes may evolve more rapidly than autosomes due to selection on expressed recessive alleles. Quantifying the effect empirically usually requires numerous assumptions due to the impact of diplodiploid transmission dynamics, and so the relative contribution of dominance effects to sex chromosome evolution remains unclear. Springtails present a novel opportunity to ameliorate this. Male globular springtails have hemizygous X chromosomes, diploid autosomes, and eliminate their paternal genome during spermatogenesis. This leads to the autosomes matching the X chromosomes haplodiploid transmission. Hence, theoretically the X chromosomes and autosomes only differ in the fixation probability of male-beneficial alleles. We generated whole-genome resequencing and RNA-Seq data for the globular springtail Allacma fusca, to quantify the faster-X effect, leveraging this natural experiment. We find that after accounting for the deleterious distribution of fitness effects, and despite surprisingly depleted neutral X-linked diversity, the sex chromosomes show signals of both stronger purifying and positive selection, supporting the faster-X effect. Furthermore, we provide the first direct evidence for the loss of DNA methylation in Collembola. These results, obtained from a system where many of the confounding sex-autosome differences that typically obscure faster-X patterns are absent, support hemizygosity as a genuine driver of sex chromosome evolution and suggest that sex-linked genes could contribute disproportionately to adaptive potential.

Genetic drift and natural selection jointly shape how populations evolve during range expansion, yet their joint influence on fitness at expanding range margins is rarely examined. Serial founder events during range expansion may amplify genetic drift and result in the accumulation (or greater expression) of deleterious mutations at range margins, termed expansion load. Conversely, natural selection should lead to local adaptation during expansion provided that populations harbor adequate genetic variation. We used a manipulative transplant experiment, genome-wide SNP data, and demographic surveys of the invasive plant, commontansy (Tanacetum vulgare), to evaluate evidence for expansion load and local adaptation during ca. 150 years of invasion in Minnesota, U.S.A. The common garden occurred near the southern range margin and included 16 populations that span (1) a chronosequence of invasion from northeastern MN (invasion core) to southern and western range margins and (2) environmental gradients in temperature and precipitation. We also manipulated temperature and precipitation to test whether environmental stress amplified the expression of expansion load or revealed population differentiation in climate adaptation. Population fitness declined strongly with distance from the invasion core, consistent with the accumulation of expansion load. This finding was corroborated by analyses of 173 populations that showed an increase in homozygosity (F) and a decrease in population size from the invasion core to range margins. We did not find any evidence of local adaptation; a strong positive relationship between population mean fitness and environmental distance was indicative of maladaptation. While the elevated temperature manipulation reduced fitness, it did not amplify the expression of expansion load. Taken together, our results are consistent with the hypothesis that serial population bottlenecks and strong genetic drift led to expansion load and reduced fitness at range margins. Teaser TextSpecies geographic ranges are dynamic over geologic time scales but may also shift rapidly in response to climate change and for invasive species. While range shifts are often viewed only through an ecological lens, the extent and pace of range expansion may be significantly modulated by evolutionary processes. We disentangled the influence of genetic drift and natural selection on population fitness across an invasion chronosequence (spanning ca. 150 years) for the herbaceous plant common tansy (Tanacetum vulgare). Our synthesis of analyses of a field transplant experiment, genome-wide SNP data, and demographic surveys provided evidence consistent with the accumulation of expansion load at leading range edges. While theory often predicts that local adaptation should occur readily in response to novel environments, our results were consistent with local maladaptation. Our findings emphasize the importance of stochastic processes in shaping the geographic distribution of species and their capacity to shift with changing environments.

Emerging infectious diseases constitute a major health threat and are often associated with zoonotic spillover processes. Pathogen host shifts may involve evolutionary adaptation to new host species, which is of central concern in relation to future pandemics. Evolutionary host shifts require certain conditions to be met, including physiological and ecological factors. A pathogen strain infecting a new host species to which it is not well adapted will generally experience reduced success, which depends on the effective similarity between the new host species and the original reservoir host species from the pathogen's perspective. The adaptation process involves intermediate strains, or phenotypes, that exist at the cost of reduced transmission and replication rates, and the evolutionary outcome depends on factors associated with host species physiology and population interactions. The interplay between host similarity and interaction, and pathogen adaptation trade-offs, is therefore important in steering pathogen evolution and possible evolutionary host-shift outcomes. Here we apply niche-evolution theory to host-pathogen systems to investigate the combined effect of host species similarity and intra- and interspecific interactions on evolutionary host shifts. We identify the conditions under which evolutionary host shifts occur and show, for a two-host-species system, that evolutionary outcomes fall into four distinct categories.

Extreme climatic events (ECEs) could potentially induce episodes of rapid adaptive evolution, altering the evolutionary trajectories and viability of wild populations experiencing increasingly stochastic environments. Adaptive potential stems substantially from additive genetic variance (V) in survival. However, the degree to which ECEs impact this variance, and the resulting evolutionary implications, have not been fully conceptualised or quantified in nature. These aims are highly challenging because underlying genetic and environmental variances have fundamentally non-linear effects on the dichotomous phenotypic outcome of survival versus death, while substantial data are required for estimation. We present a conceptual and analytical framework that formalises biological hypotheses for how V depends on environmental severity, how such dependences are reshaped by non-linear genotype-environment-phenotype relationships and demographic structure, and the implications for evolutionary responses. We then use 25 years of survival and pedigree data from European shags (Gulosus aristotelis) to decompose variance in adult survival across diverse environmental conditions including ECEs. Using a capture-recapture animal model, we demonstrate non-negligible V underlying adult survival across all years combined, implying notable adaptive potential. Yet, partitioning by environmental severity revealed substantial V in good years with high survival but negligible V in bad years with ECE-induced low survival, implying a genotype-by-environment interaction that constrains adaptive potential under severe conditions. However, scale transformations showed how the non-linear genotype-environment-phenotype relationship can distort or even reverse such patterns, by reducing the extent to which V is phenotypically expressed in good conditions with high mean survival and amplifying it in more severe conditions with lower mean survival. Evolutionary responses to severe conditions could consequently be non-negligible even given small underlying V. We thereby demonstrate how ECEs can reshape adaptive potential, highlighting the need to integrate impacts of environmental severity on genetic variation in fitness components into predictions of population resilience under climate change.

Population divergence with gene flow has proven more common than expected, but the underlying mechanisms are not fully understood. Magic traits (i.e. characters involved in both ecological adaptation and assortative mating) offer a tantalizing mechanism to explain the phenomenon, yet empirical demonstrations are rare. Moreover, speciation is assumed to involve genomic processes that couple multiple reproductive barriers, rather than being driven by a single barrier, and it re-mains unclear how magic traits interact with these processes. Here, we investigate the marine midge Clunio marinus, whose reproduction is timed to the extreme spring tide low tides during full moon or new moon. In Roscoff (Brittany, France) there are two sympatric chronotypes, i.e. subpopulations which reproduce only during full or new moons. Lunar reproductive timing is hypothesized to act as a magic trait, as it is both ecologically relevant and isolates reproduction in time. Based on wild-caught mating pairs and laboratory crosses, we show that lunar timing indeed is the major reproductive barrier (RI > 0.87). We also identify additional barriers which further increase reproductive isolation (total RI > 0.94). To explore the genomic basis of these barriers, we perform association testing on several high-FST loci. Two loci were associated with multiple barriers, and patterns of linkage disequilibrium suggest that these effects may arise from a combination of genetic link-age and pleiotropy. Together, our results indicate that lunar timing played a pivotal role in chronotype divergence, not only as a magic trait but also by promoting the recruitment of additional isolating barriers. We hypothesize that this recruitment is due to the polygenic and complex genetic architecture of lunar timing, highlighting the joint role of magic traits and genomic architecture in divergence with gene flow.

A central mechanism of sexual selection theory is Fisher's process, which refers to the coevolution of male traits and female preferences, in which preference is indirectly selected through genetic association with male trait alleles built up via mate choice. However, empirical studies often fail to detect strong trait-preference genetic correlations, raising doubts about the importance of Fisherian selection in nature. Notably, the theoretical expectation that genetic correlations are essential for trait-preference coevolution through Fisherian selection derives largely from models assuming infinitely large populations, whereas real populations are finite. Using population genetic models, I show that interactions between Fisherian selection and genetic drift can fundamentally decouple trait-preference genetic correlations from the evolution of male traits and female preferences. Genetic drift generally reduces expected trait-preference correlations but simultaneously promotes the expected increase in female preference frequency beyond deterministic predictions. Consequently, in populations of realistic sizes, trait-preference correlations may often be weak or even negative, particularly when recombination among trait and preference loci is infrequent, but substantial trait-preference coevolution can still occur. Therefore, the strength of genetic correlations may be an unreliable indicator of the extent of trait and preference coevolution, offering a potential resolution to a longstanding dilemma in sexual selection theory.

Host-microbiota interactions are crucial in adapting to environmental changes, such as fluctuating energy availability. Yet, the extent to which hosts and their microbiota exhibit coordinated plasticity in response to transient energy limitation remains unclear. Here, we examined the capacity for parallel reversible plasticity in hosts and gut microbiota to temporary dietary restriction in hosts with differing energy needs. We subjected bank voles (Clethrionomys glareolus) from a long-term artificial selection experiment for high aerobic metabolism (A-lines) and control lines (C-lines) to dietary restriction (food dilution with insoluble fiber) followed by a recovery period. We measured traits relevant for vole energy consumption and fecal microbiota composition at baseline, after dietary restriction, and after recovery. We hypothesized that A-line voles would experience more severe and prolonged physiological effects of dietary restriction than C-line voles, which might be counteracted by higher microbiota responsiveness. Dietary restriction caused a temporary increase in food consumption, decrease in body mass and resting metabolic rate, and significant shifts in gut microbiota composition, all of which returned to near baseline levels during the recovery period. These effects were largely similar for the selection lines, but contrary to our prediction, the effect of dietary restriction on bacterial diversity was stronger in C-lines. This suggests higher resistance of the A-line microbiota to dietary changes, perhaps resulting from increased host control over microbial communities due to the directional selection for high metabolic capacity. Overall, our findings highlight a substantial capacity for reversible plasticity in host physiology and gut microbiota in fluctuating environments.

Herbicide resistance is among the clearest examples of rapid adaptation to intense anthropogenic selection. Yet, how the evolutionary origins and genetic architecture of resistance shapes its tempo and mode of evolution remain incompletely resolved. Here, we address these questions in Alopecurus myosuroides (blackgrass), Europe's most widespread and economically damaging herbicide-resistant weed. We present the first genome-wide analysis of herbicide resistance in natural blackgrass populations, uniquely combining historical and contemporary populations collected before and after the onset of intensive herbicide use. This temporal framework provides novel empirical access to pre-selection genetic variation, enabling reconstruction of the tempo and mode of both target-site (TSR) and non-target-site resistance (NTSR) evolution across space and time. TSR mutations were not found in pre-herbicide populations and evolved recently through repeated, largely independent origins across Europe. NTSR, in contrast, has a polygenic architecture and is associated with a cluster of glutathione S-transferases (GSTs) with signatures of copy number variation, and broader stress-response genes. Most NTSR-associated alleles were already segregating in historical populations, consistent with rapid adaptation from standing genetic variation. Moreover, resistance-associated loci show signatures consistent with positive selection predating herbicide use, suggesting these stress and detoxification pathways were historically maintained by prior ecological selection and subsequently recruited under herbicide pressure. Together, these findings demonstrate that herbicide resistance encompasses contrasting genetic routes, with polygenic NTSR evolving largely through selection on standing variation, offering broader insights into the evolutionary dynamics of rapid polygenic adaptation under novel anthropogenic selection.

Mutation-selection balance is the most plausible general mechanism for the maintenance of additive genetic variance (VA) for quantitative traits in natural populations. It is well established that the genetic variants affecting traits (QTLs) are widely distributed across species' genomes. At the same time, unconditionally deleterious mutations are also expected to be common, with those with the largest fitness effects tending to be strongly recessive. Many genomes possess regions of restricted recombination that could result in tight linkage between largely recessive deleterious alleles, conditions which can lead to elevated heterozygosity via associative overdominance (AOD). Here we show that weakly selected QTLs linked to genomic regions exhibiting AOD can elevate VA above what is expected in the absence of unconditionally deleterious mutations. Selection on traits when VA is maintained by AOD, however, may expose recessive deleterious alleles as homozygotes, reducing fitness. Thus, while AOD may contribute to the maintenance of VA, variation maintained in this way may not be readily accessible by natural or artificial selection.