Heredity

Heat Shock Protein 90 (HSP90) functions as an evolutionary capacitor, allowing populations to store cryptic genetic variation that can be released under stress. While former studies have described the release of morphological variation, its behavioural consequences remain unexplored. In the red flour beetle, Tribolium castaneum, HSP90 inhibition released a phenotype with much smaller, less defined eyes that confers fitness benefits in continuous light and was subsequently assimilated. We hypothesized that altered eye morphology affects light perception and thereby changes light-dependent behaviours. To test whether phenotypes released via evolutionary capacitance can beneficially alter behaviour, we examined locomotor activity rhythm entrainment to light-dark cycles as well as individual and group light choice behaviour. Males of the reduced-eye phenotype exhibited a diminished startle response to sudden light exposure in locomotor activity assays. We also found reduced negative phototaxis in groups of beetles with reduced eyes. This modified behaviour, indicating reduced light sensitivity, may stem from impaired light perception caused by altered eye morphology. Lower light sensitivity could be beneficial under stressful environmental conditions by promoting the exploration of alternative niches. Therefore, this study provides the first evidence for potentially beneficial behavioural changes in a HSP90-released phenotype, reinforcing HSP90s role as an evolutionary capacitor.

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.

Whole genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects. The resulting morphological, physiological, and fitness consequences and how they affect the survival probability of newly polyploid lineages are intensively studied, but very little is known about the effect of genome doubling on the short-term evolvability of populations. Understanding the effect of polyploidization on the adaptive potential of populations is of crucial importance to predict the future of polyploid populations. In this paper, I investigate the immediate consequences of genome doubling on the genetic variance of populations. To do so, I performed numerical iterations and simulations of how the genetic variance of a quantitative trait changes after polyploidization, under different genetic architectures (additivity, dominance, and epistasis). I found that genetic variance generally decreases after genome doubling. Non-additive gene actions can make autotetraploid populations genetically more diverse than their diploid progenitors in rare cases, notably with overdominance and directional epistasis. By collecting estimates from the agronomic literature, I found that both dominance and epistatic variance contribute to the genetic variance of polyploid populations. These results bring new insights into the adaptive potential of newly formed tetraploid populations, and call for further experimental investigations of how polyploidization is associated with a short-term decrease in evolvability.

Recombination rate varies within and between individuals. One form of such variations is seen between sexes in dioecious populations, with males typically exhibiting a smaller recombination rate than females. This is true both for sex chromosomes and autosomes (so-called heterochiasmy). Although a large body of theory exists on the role of sex chromosomes in adaptation and population divergence, much less is known about the role of heterochiasmy. Recently, it has been suggested that heterochiasmy can facilitate local adaptation and divergence, but if, and when this is true has not been systematically studied theoretically to date. Here we use Individual-based simulations to assess the effect of sex differences in autosomal recombination rates on the process of divergence and adaptation in populations subject to divergent selection and migration. We found evidence supporting that sex differences in autosomal recombination rate between adaptive loci can facilitate, and especially maintain, divergence, but this is true only under very limited conditions, involving strong selection, high sex-averaged effective recombination rates and relatively high rates of migration compared to the strength of selection. We further found that this effect, when present, is typically weak but is amplified in cases of highly polygenic adaptation in comparison to cases with a few adaptive loci of strong effect. We conclude that, in most cases, sex differences in autosomal recombination rate alone are unlikely to noticeably contribute to the process of adaptation and divergence. Further studies are needed to evaluate their effect in combination with other processes not considered in the present study, such as assortative mating between the alike mates, or recombination suppression in heterozygotes. TeaserIn dioecious populations, recombination rate typically differs between males and females. This is true both for sex chromosomes and autosomes. While much theoretical research has focused on understanding how recombination rate differences in sex chromosomes shape local adaptation and divergence, we lack theoretical knowledge of the potential role of sex differences in autosomal recombination rates. Recombination has a dual role in local adaptation. Strong recombination can effectively purge deleterious alleles, but it can also break apart beneficial allele complexes (and vice versa for weak recombination). Thus, one may expect that in the presence of both strong and weak recombination exhibited by females, and males, respectively, population divergence can be efficiently facilitated. But is this true? Here, we study this question theoretically using computer simulations. Our main finding is that sex differences in autosomal recombination can facilitate divergence, but this effect is typically weak and present only under very stringent conditions.

Deciphering the genetic architecture of complex quantitative phenotypes remains challenging in quantitative genetics. These traits not only depend of multiple genetic factors but are also established over time and environments. Although quantitative genetics has investigated the genetic determinism of phenotypic plasticity in contrasted environmental conditions, the time related phenotypic plasticity has received less attention. Here we proposed a multivariate Bayesian framework, the Bayesian Varying Coefficient Model, designed for analysing the genetic architecture of the time related phenotypic plasticity by a multilocus approach. We applied the BVCM to time series phenotypes measured at various time scales (daily, monthly, yearly) across a diverse set of biological species. We included in this study: yeast (Saccharomyces cerevisiae), fungi (Fusarium graminearum), eucalyptus (Eucalyptus urophylla x E. grandis), and sweet cherry tree (Prunus avium). The BVCM results were compared with those obtained with a known genome-wide association method carried out time by time. For all species and traits, the BVCM was able to detect the major QTL identified by marker-trait association methods and revealed additional genetic regions of weak effect. It also increased the phenotypic variance explained for most of the phenotypes considered. It revealed dynamic QTLs with transitory, increasing or decreasing effects over time. By considering both the temporal and genetic multivariate structures in a single statistical model, we increased our understanding of the genetic architecture of complex traits notably by reducing the issue of missing heritability. More broadly, this work raises the foundation for extended applications in functional genomics, evolutionary ecology, and crop breeding programs, in which time-related phenotypic plasticity remains crucial for predicting and selecting key quantitative complex traits. Key messageBy capturing the genetic factors influencing the time related phenotypic plasticity, our approach contributes to a deeper understanding of the dynamic nature of genotype-phenotype relationships.

The ectoparasitic mite Varroa destructor is the most significant parasite of the Western honey bee (Apis mellifera) and a major driver of colony losses worldwide. Although extensive research has focused on behavioral and physiological mechanisms of host resistance, comparatively little attention has been paid to potential phenotypic responses of the parasite itself. Here we investigated body size variation in Varroa destructor associated with varroa-resistant and non-resistant honey bee colonies across four European countries. We quantified the dorsal shield area of adult female mites from multiple colonies differing in the honey bee colonies resistance status, using standardized digital image analysis. Across geographically distant non-resistant populations, mite body size was remarkably consistent, with a median dorsal shield area of 1.47 mm2. In contrast, mites originating from varroa-resistant colonies were consistently smaller, with a median dorsal shield area of 1.37 mm2, representing an approximately 6.8% reduction in body size. This pattern was reproducible across different geographical areas, honey bee genetic backgrounds and beekeeping practices. The striking stability of mite body size in non-resistant populations contrasted with the consistent reduction observed in mites associated with resistant hosts, suggesting a host associated shift in parasite phenotype. Because body size in arthropods integrates developmental conditions, nutritional availability and resource allocation, the observed pattern may reflect altered developmental environments and selective pressures imposed by resistant hosts. Our results show a consistent morphological shift in this globally important parasite associated with resistant hosts and suggest that dorsal shield size in Varroa could serve as a new selection marker for varroa-resistant honey bee colonies.

Trees accumulate somatic mutations throughout their long lifespan, resulting in genetic mosaicism among branches. While recent genomic studies quantified these mutations, they were largely limited to describing static patterns of variation. In this study, we developed a mathematical model to infer the dynamic processes of somatic mutation accumulation from snapshot genomic data obtained from four tropical trees (Dipterocarpaceae), which dominate tropical rain forests in Southeast Asia. Our model focus on genetic differences between shoot apical meristems (SAMs) at branch tips and explicitly incorporate stem cell dynamics within SAMs during shoot elongation and branching, enabling us to quantify somatic genetic drift arising from stem cell lineage replacement. By comparing model predictions with empirical data from Dipterocarpaceae trees, we estimated key parameters governing stem cell dynamics and somatic mutation rates. Our results indicate that both shoot elongation and branching involve replacement of stem cell lineages, leading to a moderate degree of somatic genetic drift. Accounting for stem cell dynamics resulted in slightly lower mutation rate estimates than previous approaches that ignored these processes. Using the estimated parameters, we further performed stochastic simulations to predict patterns of somatic mutations, including features not directly observed in the sampled trees, such as occasional deviations of somatic mutation phylogenies from physical architecture. Together, our modeling framework provides insights into how genetic mosaicism is shaped within tropical trees and reveals the stem cell dynamics underlying their long-term growth and accumulation of somatic mutations. (236 words) Highlights- We built mathematical models to predict the genetic differences between branch tips by somatic mutations. - The model considers the varying dynamics of stem cells in shoot meristem during shoot elongation and branching. - We compared the model prediction with empirical data from tropical trees, Dipterocarpaceae, and estimated the dynamics of stem cells and mutation rate. - Somatic mutation dynamics were shaped by somatic genetic drift arising from stem cell lineage replacement during shoot elongation and branching. - Accounting for stem cell dynamics led to slightly smaller estimates of mutation rates compared with previous estimates that ignored the dynamics. - Our models offer insights into how genetic variability is shaped in the tropical trees and the stem cell dynamics underlying their long-term growth.

Interest in quantifying linkage disequilibrium (LD, non-random associations of alleles at different loci) has skyrocketed in recent years as researchers have focused on use of LD in genome-wide association studies (GWAS), for studying historical demography, and for estimating effective population size (Ne). The most widely used LD metric is r2 = the squared correlation of alleles at a pair of loci. Despite a half century of efforts, developing an unbiased expectation of r2 as a function of the many factors that can affect it (physical linkage, genetic drift, selection, migration, mutation, mating systems) remains elusive. Furthermore, even when all of these other factors are absent, empirical estimates of r2 are upwardly biased by sampling a finite number (S) of individuals, and that must be accounted for if one wants to focus on the desired signal of LD. Previous approaches to estimate [Formula] have been shown to be biased to greater or lesser degrees. The purpose of this short paper is to demonstrate that a simple and apparently exact expression for [Formula] does exist for the special case where sampling error is the only factor contributing to r2, in which case [Formula] = 1/(S - 1). When other factors contribute heavily to LD, [Formula] shrinks toward 0 as empirical r2 [->] 1. However, for estimating contemporary Ne with unlinked markers, empirical r2 will generally be small and 1/(S - 1) will provide a robust estimate of [Formula].

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.

Genotype-by-environment interaction (GEI) has been studied to identify environment-stable/favorable genotypes. The GEI simulation could help refine the inference by incorporating tangible factors such as genomic and environmental information. The Bayesian additive main effect and multiplicative interaction (Bayesian AMMI) model captures the genotype-specific responses across environments, reflecting directional relationships between genotypes and environments. Thus, we propose a Bayesian AMMI-based GEI simulation framework that utilizes high-throughput environmental covariance matrices to generate GEI effects with interpretable directional structure. To demonstrate the proposed approach, two simulated phenotypes were assessed under four levels of GEI variance. In the first simulation (Sim1), GEI effects were sampled from a multivariate normal distribution defined by the GEI matrix. In the second simulation (Sim2), GEI effects were generated by extending Sim1 with the Bayesian AMMI model. In both simulations, increasing GEI variance resulted in lower correlations of phenotypes across environments and stronger genotype-specific sensitivity to environmental variation. Across five cross-validation designs, models accounting for GEI consistently outperformed one that did not, with prediction accuracy generally decreasing as GEI variance increased. Clear distinctions between the two simulated phenotypes were evident from biplot analyses: Sim2 successfully captured environmental relatedness and genotype-specific responses, whereas such structure was absent in Sim1. These results demonstrate that the proposed Bayesian AMMI-based GEI simulation framework enables interpretable visualization of GEI and supports genomic selection strategies under complex environmental conditions.

O_LIWhen species hybridize, resistance to introgression is presumably due to selection against hybridizing alleles. While many studies have characterized direct selection at these sites, alleles may resist introgression through correlational selection. Here we investigate the role of direct and correlational selection in reducing introgression at the color locus in Ipomoea cordatotriloba. C_LIO_LIWe used recombinant inbred lines that varied in limb color, flower size and sugar concentration to estimate the fitness advantage of the flower color allele via direct and correlational selection. To assess the effect of correlational selection on fitness, we ask if floral size or nectar sugar concentration is correlated with fecundity in pink- but not white-limbed lines. C_LIO_LIWe find no evidence for direct selection on flower color across four fitness components - germination, survival, fecundity, and siring success. Instead, both flower size and sugar concentration significantly correlate with fecundity in pink, but not white limbed lines. As a result, correlational selection on the color allele opposes introgression when recurrent migration is low (<3%). C_LIO_LIThese results demonstrate that correlational, rather than direct, selection is sufficient to resist introgression via hybridization and suggest that correlational selection is an underexplored mechanism to generate resistance to introgression across multiple loci. C_LI

The fungal crop pathogen Blumeria hordei, causal agent of powdery mildew on barley, presents life-history and epidemiological characteristics, as well as and selective pressures due to modern agriculture leading to expected sweepstakes reproduction, that is highly skewed offspring distributions. Using genome-wide polymorphism data and population genomics inferences, we aim to 1) infer the past demographic history and the strength of sweepstakes reproduction in B. hordei, and 2) quantify the contributions of these selective and neutral processes in the genome. An new inference method based on Neural Posterior Estimation and diversity and linkage disequilibrium statistics was developed and tested on simulated and B. hordei genomic data. We confirm that B. hordei exhibits a moderate sweepstakes reproduction (-parameter of 1.6). We highlight that the Site Frequency Spectrum (SFS) appears sensitive to the joint occurrence of sweepstakes and recent demographic changes, which may caution on the reliability of the SFS to infer sweepstakes reproduction. We then scan the genome for selective sweeps, adjusting the significance thresholds of the methods for demographic history and sweepstakes reproduction, thereby yielding a counterintuitive result. When conditioning the significance threshold for sweep detection on simulations under sweepstakes and demography, a very large number of putatively selected regions is found (11.6% of the genome). We suggest that sweepstakes reproduction in B. hordei is due to 1) neutrality (clonal/sexual phases and Boom-and-Bust cycles) generating a genome-wide level of background noise in the coalescent genealogies, and 2) selective sweepstakes due to pervasive positive selection. Our findings have important implications for both population genomic methodology and our understanding of pathogen evolution.

Climate warming alters the thermal environment experienced by ectotherms, whose physiological performance and fitness are constrained by temperature. Early life stages are often the temperature-sensitive phases of the life cycle, with potential consequences for population persistence, particularly in freshwater stenotherms such as the Arctic charr (Salvelinus alpinus). The persistence of populations will partly depend on the adaptive potential of critical life stages to environmental changes. In this study, we used a common garden approach to compare the response and phenotypic plasticity of four charr populations to warmer conditions. These populations inhabit thermally contrasted lakes and differ in origin (native/introduced) and management history. We reared embryos at either an optimal (5{degrees}C) temperature for larval development or a warmer but realistic (8.5 {degrees}C) temperature. We tested adaptive divergence among populations in four traits (survival, incubation duration, body length and yolk sac volume), using Qst - Fst comparisons. We report negative effects of temperature on body size, survival and earlier hatching. Thermal reaction norms differed among populations, indicating adaptive divergence. Contrary to expectations, populations originating from warmer environments did not consistently exhibit higher trait values under elevated temperatures. In contrast, the unmanaged and colder high-altitude population exhibited higher survival rates and lower yolk reserves for a given size under heat stress than the other populations. Our results suggested that evolutionary trajectories specific to each population are shaped by factors related to the populations history, including introductions, demographic fluctuations and long-term repopulation practices, which can jointly influence the potential for adaptation to heat stress.

Longitudinal data on disease susceptibility in forest trees are rare but essential for understanding host-pathogen dynamics and genetic variation in susceptibility traits. We present a long-term multisite common garden dataset quantifying susceptibility of Scots pine (Pinus sylvestris) to Dothistroma needle blight. The dataset comprises annual disease assessments collected from the same trees across 11 years, spanning 168 families and 21 Scottish provenances. This design enables partitioning of genetic and environmental sources of variation, evaluation of temporal stability in host response, and estimation of variance components and narrow-sense heritability of susceptibility. The data support analyses of phenotypic plasticity, provenance-level responses, and interactions between disease susceptibility and other adaptive traits. This resource will facilitate predictive modelling of host susceptibility under current and future environmental conditions.

Many simultaneous hermaphrodites use selfing for reproductive assurance only when outcrossing opportunities are limited, owing to inbreeding depression in selfed progeny. However, scenarios that enforce substantial selfing (such as during recolonisation) can rapidly select for a high selfing propensity, a shift in mating system that is expected to eliminate both inbreeding depression and the delayed reproductive onset under selfing that is typically associated with it. We tested these predictions in the flatworm Macrostomum hystrix, using a line derived from an outcrossing population that had been subjected to enforced selfing for multiple generations followed by several years of relaxed selection. As predicted, isolated individual forced to self and individuals with constant partner access (i.e. outcrossing opportunities) did not differ in reproductive onset nor in inbreeding depression estimated through offspring survival. However, a third treatment group that provided intermittent partner access (to allow outcrossing but minimise potential competition effects) showed a different pattern: no inbreeding depression in offspring but a substantially accelerated reproductive onset. Whilst our results thus support the effective purging of inbreeding depression and increased selfing propensity under enforced selfing, we suggest that cues of an unstable social or physical environment nevertheless exert a major influence on reproductive timing.

Epimutations are changes in chromatin modifications, such as DNA methylation or histone modifications. Some of these epigenetic changes can be inherited for several generations, and they potentially contribute to evolutionary processes. Estimates of epimutation rates now exists in a few species, but the presence and function of epigenetic marks are not conserved across different species. To understand the properties of epimutations in fungi, we performed a mutation accumulation experiment with the filamentous fungus Neurospora crassa and investigated spontaneous changes in DNA methylation and trimethylation of lysine 9 on histone H3 (H3K9me3) in the mutation accumulation lines. We observed that centromeric regions are hotspots of spontaneous DNA methylation changes in N. crassa. In these hotspot regions, DNA methylation changes were transmitted across mitoses, but changes occurring in euchromatin were not maintained. The rate of DNA methylation changes was around 30 000 fold faster than the genetic mutation rate. We did not observe spontaneous changes in H3K9me3 that were transmitted across mitoses. Our results show that while spontaneous epimutations occur in this species, they occur predominantly in gene poor heterochromatic regions, so their impact for evolutionary adaptation may be limited.

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.

Life history traits are often correlated, creating trade-offs that may impede the response to natural selection and be responsible for the evolution of senescence. These trade-offs may arise through pleiotropic effects, which can affect the response to selection in ways that resemble intra-locus sexual antagonism. Despite these hypothesized relationships, we lack clear connections between pleiotropy, sexual antagonism, and the evolution of life histories. Empirical tests for inter-sexual differences in life-history traits, including sex-specific aging, can be used to evaluate hypotheses about how pleiotropy and sexual conflict affect evolutionary trade-offs. To those ends, we measured lifespan, development time, and body size in Drosophila pseudoobscura males and females, each of which carried one of six third chromosome inversion genotypes. Temperature affected lifespan and development more than any other factor; higher temperatures increased mortality rate, decreased lifespan, and accelerated development. However, we also observed sex differences in mortality rates and development times that depended on genotype and temperature. Notably, temperature elevated the initial mortality rate across all flies, yet increasing temperatures reduced the rate of aging in some genotype-sex combinations. Similarly, direct effects of genotype on mortality rate and development time depended greatly on sex and temperature, but there was no genotype effect on body size. Despite these context-dependent genotype effects on life history traits, we failed to identify any correlations that would serve as clear evidence for sexual conflict or trade-offs. Our results therefore suggest that either historical conflicts have been resolved or any conflicts that may exist do not result in the correlations predicted by existing models.

In quantitative genetics, candidate SNPs are identified through genotype-phenotype associations inferred with genome-wide association studies (GWAS). In this study, we explore an alternative approach to detect genetic variants with non-neutral effects by tracking temporal trends in allele frequency in a winter wheat (Triticum aestivum L.) breeding population over an eight-year period, from which signals of selection may be inferred. Selection signatures were inferred with a generalized linear model, where we modeled trends in allele frequency as a function of time (crossing year). These signatures of selection were used to prioritize variants. Associations between phenotypic performance and individual load of prioritized variants were then investigated. Furthermore, we assessed whether incorporating selection information into a genomic best linear unbiased prediction (GBLUP) model improves model performance in terms of quality of fit and prediction ability. Our findings indicate that the inferred signals of selection are effective in identifying non-neutral variants. Variants under strong negative selection were associated with a decrease in protein content adjusted for grain yield (p-value < 0.01), while genetic variants that had been under moderate to high levels of positive selection were associated with increased grain yield (p-value < 0.01). However, incorporating selection information did not improve prediction accuracy. In conclusion, temporal trends in allele frequency can be used to detect non-neutral variants. The proposed approach may hence complement traditional quantitative genetic methods for detecting non-neutral genetic variation. This approach may allow breeders to detect non-neutral variants earlier in the breeding cycle, without resorting to phenotypic data.

Sex ratio distorters (SRDs) are heritable elements that bias offspring sex ratios to enhance their transmission. In the terrestrial isopod Armadillidium vulgare, feminization of genetic males can occur through vertical transmission of the sex ratio distorter known as the f-element, as well as through infection by Wolbachia, a maternally inherited bacterial endosymbiont that can alter host reproduction. Previous studies have focused on the distribution of SRDs and their associations with mitochondrial haplotypes in native European populations, but these patterns are poorly understood in the United States. In this study, we sampled A. vulgare in 12 states, screening individuals for Wolbachia infection, the presence of the f-element, and mitochondrial haplotypes. We found that Wolbachia shows a heterogeneous distribution across populations and haplotypes, in contrast with stronger associations in Europe. The f-element occurred in lower overall frequencies but showed a strong association with mitochondrial haplotype VI. These results indicate that patterns associated with SRD differ from those observed in Europe and suggest that multiple introductions and population mixing have shaped these distributions.