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Statistics of adaptive walks under a moving fitness optimum. (A) Ratio of the average lag in fitness (λ) between the population and the optimum in haploids (hap) and diploids (dip) as a function of the speed of environmental change. In fast-changing environments, diploid populations follow the moving optimum more closely than haploids (λ hap /λ dip > 1). (B) Fitness variance attributable to balanced polymorphisms (frequency 0.05 < x < 0.95) and the age of the balanced polymorphism for different values of σ env. Both quantities are estimated from the balanced polymorphisms that were present at the end of simulation runs. The age of a balanced polymorphism is defined as the time since the most recent common ancestor of its constituent alleles. Data points are medians over 10 3 runs, and error bars specify the 10% and 90% quantiles. The gray-shaded area (0.04N < age < 4N) indicates the expected age range of common neutral polymorphisms at frequencies between 0.05 < x < 0.95. (C) Same as in B but phenotypic variance is shown instead of fitness variance.
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Molecular adaptation is typically assumed to proceed by sequential fixation of beneficial mutations. In diploids, this picture presupposes that for most adaptive mutations, the homozygotes have a higher fitness than the heterozygotes. Here, we show that contrary to this expectation, a substantial proportion of adaptive mutations should display hete...
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Citations
... Of these SNPs, including three in European seabass and one in gilthead sea bream, the heterozygous genotypes were associated with the preferable phenotype, i.e., a lower enzymatic activity compared with both homozygous genotypes [60]. This phenomenon is likely due to a decrease in enzymatic activity or protein stability in the heterozygous state, resulting in a lower response phenotype [61]. Conversely, the remaining six SNPs in European seabass and two SNPs in gilthead sea bream displayed a dominant/recessive interaction, where one of the homozygous genotypes had a significantly lower response compared with the other homozygous genotype and the heterozygote [62]. ...
In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.
... Previous work has shown that this model can generate heterosis, with or without coadaptation (Barton, 2001;Chevin et al., 2014;Simon et al., 2018;, and that it can generate transient overdominance -i.e. overdominance that comes and goes with changes in the genetic background (Manna et al., 2011;Sellis et al., 2011). It therefore has the potential to mislead tests of the theories of heterosis using introgression lines. ...
... The results in Figure 2B-D arise because, when D > n, mutations will often act in similar phenotypic directions, and so show fitness interactions in some genetic backgrounds. Nevertheless, the results do not imply an intrinsic advantage to heterozygosity, but instead represent the transient overdominance that arises naturally with optimizing selection (Manna et al., 2011;Sellis et al., 2011). In recombinant hybrids, derived mutations will be deleterious on average, whether in 9 . ...
... We have shown that this model can mislead the most straightforward tests of fixability -especially when there is a high variance in the selective effects, and variable fitness interactions between pairs of alleles ( Figure 2). While the classical theories of heterosis have distinguished between true overdominance and associativeor pseudo-overdominance (Shull, 1908;East, 1908;Bruce, 1910;Keeble and Pellew, 1910;Jones, 1917;Collins, 1921;Crow, 1948), this model suggests a third possibility: transient overdominance (Sellis et al., 2011;Manna et al., 2011), where single mutations can be overdominant, but in a way that is strongly background dependent, such that the overdominance will come and go in recombinant hybrid genotypes. Transient overdominance, with or without coadaptation, can arise under the process posited by the classical dominance theory, i.e., the fixation of recessive deleterious mutations via genetic drift. ...
Many species pairs form F1 hybrids that are fitter than their parents. Such heterosis can arise if the parents carry recessive deleterious mutations; and in this case, the heterosis should be fixable, because selecting out the deleterious mutations yields a high-fitness homozygous hybrid. However, heterosis might not be fixable if caused by overdominance (an intrinisic advantage to heterozygosity) or if the parents contain coadapted gene complexes. These alternatives have been tested with introgression lines, where small regions of genome are scored in the heterospecific background. We develop predictions for introgression line data under a simple model of phenotypic selection, where parents diverge by fixing deleterious mutations via genetic drift. We show that this simple process can generate complex patterns in the data, misleading tests for both overdominance and coadaptation. We also suggest new ways to analyse the data to overcome these difficulties. Reanalyses of published data from Solanum and Gossypium suggest that the model can account for the qualitative patterns observed, though not the extent of apparent overdominance.
... Adaptation from standing genetic variation also favours small-effect variants (Matuszewski et al. 2015), though variants with intermediate-to-large effects are also expected to contribute to divergence following abrupt environmental changes (Hayward and Sella 2022;Devi and Jain 2023). Finally, and in contrast to early models that focused on haploid populations where adaptation proceeds by fixation of positively selected genetic variants, Sellis et al. (2011) showed that diploid populations often adapt through the spread of large-effect, overdominant mutations that are transiently maintained as balanced polymorphisms. ...
... Positive selection, which applies to mutations that yield a greater benefit in homozygous than in heterozygous state ( ), favours fixation of the established mutation. Overdominant selection, which arises when the fitness of heterozygotes is greater than both wild-type and mutant homozygotes ( ), generates short-term balancing selection during adaptation to an optimum (Sellis et al. 2011). As we show A c c e p t e d M a n u s c r i p t below, changes in population size substantially affect the relative probabilities of adaptation by these scenarios of selection. ...
... Changes in population size also affect the relative contributions of positively selected and overdominant mutations to adaptation (Fig. 2B). For all types of population size change, the probability that adaptation uses positively selected mutations decreases with mutations size (x), as previously shown by Sellis et al. (2011). Adaptation by positive selection declines more precipitously A c c e p t e d M a n u s c r i p t with x in expanding populations than in declining populations (Fig. 2B). ...
Since the rediscovery of Mendelian genetics over a century ago, there has been much debate about the evolutionary importance of mutations with large phenotypic effects. While population genetic models predict that large-effect mutations will typically contribute to adaptation following an abrupt change in environment, the prediction applies to populations of stable size and overlooks effects of population size change on adaptation (e.g., population decline following habitat loss; growth during range expansion). We evaluate the phenotypic and fitness effects of mutations contributing to adaptation immediately following an abrupt environmental shift that alters both selection and population size dynamics. We show that large-effect mutations are likely to contribute to adaptation in populations declining to a new carrying capacity, somewhat smaller-effect mutations contribute to evolutionary rescue, and small-effect mutations predominate in growing populations. We also show that the relative contributions of positively selected and overdominant mutations to adaptation depend on interactions between the phenotypic effect size distribution for new mutations and the specific form of population size change during adaptation (i.e., growth, decline, or evolutionary rescue). Our results illustrate how population size dynamics can shape the genetic basis of adaptation, which should motivate empirical comparisons of populations adapting in different demographic contexts.
... Notably, individuals with the heterozygous genotype for SIRT1 at rs12415800 in our samples had significantly lower levels of depressive symptoms. This protective effect can be attributed to the heterozygote advantage, which is a genetic phenomenon where individuals carrying two different alleles for a particular gene have an advantage over those carrying two copies of the same allele (28,32). This advantage has been observed in other genes as well, such as MAD1L1 (rs1107592) and TSNARE (rs4976976) heterozygotes who have a decreased risk of schizophrenia (29), and Ank3+/− heterozygous mice which exhibited similar behavioral alterations of reduced anxiety and increased motivation for reward when compared to wild-type Ank3+/+ mice (33). ...
Background
Previous research has linked polymorphisms in the SIRT1 gene to depressive symptoms, particularly in Chinese individuals. However, it is not clear how personality traits may contribute to this association.
Methods
To explore the potential mediating effect of personality traits, we utilized a mediation model to examine the relationship between the SIRT1 rs12415800 polymorphism and depressive symptoms in 787 Chinese college students. Depressive symptoms were assessed using the Center for Epidemiologic Studies Depression (CES-D) scale, while personality traits were measured using the Big Five Inventory (BFI).
Results
Our analysis indicated a significant association between the SIRT1 rs12415800 polymorphism and depressive symptoms, with this relationship partially mediated by the personality traits of neuroticism and conscientiousness. Specifically, individuals who were heterozygous for the rs12415800 polymorphism and had higher levels of conscientiousness were less likely to experience depressive symptoms. Conversely, those who were homozygous for the rs12415800 polymorphism and had higher levels of neuroticism were more likely to experience depressive symptoms.
Conclusion
Our results suggest that personality traits, particularly neuroticism and conscientiousness, may play a critical role in the association between the SIRT1 rs12415800 polymorphism and depressive symptoms among Chinese college students. These findings highlight the importance of considering both genetic factors and personality traits when exploring the etiology of depressive symptoms in this population.
... This related result illustrates the concept of heterozygote advantage, which corresponds to a more fit heterozygote phenotype compared to homozygotes. This concept suggests that natural selection will maintain polymorphism in the population [41]. This hypothesis could be consistent with human studies showing that heterozygosity for SNP S180L, a loss-of-function associated mutation [10], is also associated with protection against TB [14,22]. ...
Progression of tuberculosis is tightly linked to a disordered immune balance, resulting in inability of the host to restrict intracellular bacterial replication and its subsequent dissemination. The immune response is mainly characterized by an orchestrated recruitment of inflammatory cells secreting cytokines. This response results from the activation of innate immunity receptors that trigger downstream intracellular signaling pathways involving adaptor proteins such as the TIR-containing adaptor protein (Tirap). In humans, resistance to tuberculosis is associated with a loss-of-function in Tirap. Here, we explore how genetic deficiency in Tirap impacts resistance to Mycobacterium tuberculosis (Mtb) infection in a mouse model and ex vivo. Interestingly, compared to wild type littermates, Tirap heterozygous mice were more resistant to Mtb infection. Upon investigation at the cellular level, we observed that mycobacteria were not able to replicate in Tirap-deficient macrophages compared to wild type counterparts. We next showed that Mtb infection induced Tirap expression which prevented phagosomal acidification and rupture. We further demonstrate that the Tirap-mediated anti-tuberculosis effect occurs through a Cish-dependent signaling pathway. Our findings provide new molecular evidence about how Mtb manipulates innate immune signaling to enable intracellular replication and survival of the pathogen, thus paving the way for host-directed approaches to treat tuberculosis.
... We hypothesize that such mutations may be recessively lethal and thus overdominant, such that the heterozygous mutant is more fit than either homozygote. Although additional experiments will be required to determine how often adaptive mutations arise in diploid populations result in overdominance, prior work suggests that it is a common outcome (Sellis et al., 2011, Sellis et al., 2016. Change in copy number and expression of HXT6/7 is an adaptation observed in glucose limitation that was found to be overdominant. ...
Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well adapted to one environment finds itself in another, pleiotropic effects of mutations that made it well adapted to its former environment will affect its success. To better understand such pleiotropic effects, we evolved both haploid and diploid barcoded budding yeast populations in multiple environments, isolated adaptive clones, and then determined the fitness effects of adaptive mutations in “non-home” environments in which they were not selected. We find that pleiotropy is common, with most adaptive evolved lineages showing fitness effects in non-home environments. Consistent with other studies, we find that these pleiotropic effects are unpredictable: they are beneficial in some environments and deleterious in others. However, we do find that lineages with adaptive mutations in the same genes tend to show similar pleiotropic effects. We also find that ploidy influences the observed adaptive mutational spectra in a condition-specific fashion. In some conditions, haploids and diploids are selected with adaptive mutations in identical genes, while in others they accumulate mutations in almost completely disjoint sets of genes.
... Consequently, beneficial alleles are more strongly favored, and deleterious alleles more readily purged, in haploid compared to diploid genomes. On the other hand, genetic variation can be more easily maintained in diploids when heterozygotes have high fitness, which is common in the framework of Fisher's geometric model (Sellis et al., 2011). We explore the net result, comparing the speed of adaptation in diploid and haplodiploid hybrids. ...
... In part, this pattern reflects more efficient purging of deleterious mutations in haplodiploid populations than in diploid populations, leading to lower initial levels of standing genetic variation in the parental haplodiploid populations, as well as over the time course of adaptation. Another contributing factor is that evolution within Fisher's geometric model induces heterozygous advantage in diploids whenever the phenotypic effect of a mutation straddles an optimum (Sellis et al., 2011), allowing more genetic variation to be maintained in diploid than in haplodiploid populations. ...
Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher’s Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.
... Although we did not observe a significant difference for most of the genetic diversity estimates, the observed heterozygosity was higher in colonies located at the edge of the fragment. Indeed, heterozygosity is regarded as particularly important in fastchanging environments such as edge sites (Sellis et al. 2011). Given that the edge of fragments is more exposed to abiotic changes (Ries et al. 2004, Laurance et al. 2011, Christianini and Oliveira 2013, this genetic variation would confer a diversity advantage during adaptation (Sellis et al. 2011). ...
... Indeed, heterozygosity is regarded as particularly important in fastchanging environments such as edge sites (Sellis et al. 2011). Given that the edge of fragments is more exposed to abiotic changes (Ries et al. 2004, Laurance et al. 2011, Christianini and Oliveira 2013, this genetic variation would confer a diversity advantage during adaptation (Sellis et al. 2011). Additionally, the colonization of edge sites would enable species to occupy new niches, expanding the population and increasing the genetic variability (Cook 1961). ...
Habitat fragmentation is considered an important threat to biodiversity, increasing species exposure to edge effects. The Brazilian Cerrado savanna is considered a biodiversity hotspot and has been converted to small, isolated fragments due to human activities. Ant communities and colony survivorship are known to be affected by edge effects in Cerrado, but to date there is no information on the genetic diversity of ant colonies at the edge of fragmented areas. Here, we investigate if colony genetic diversity and structure of Odontomachus chelifer (Latreille) ants (Hymenoptera: Formicidae) are subject to edge effects in a Cerrado reserve in southeast Brazil. Using microsatellites, we evaluated the number of breeders (queens and males) and the genetic diversity in O. chelifer colonies located in the interior versus edge of a Cerrado fragment. All O. chelifer nests had multiple queens, which presented a low mating frequency. The number of breeders and most estimates of genetic diversity did not differ between colonies at the edge versus interior of the fragment. Genetic structure was not influenced by nest location as well. However, we detected a small and positive increase in the observed heterozygosity in colonies located at fragment edges. High heterozygosity is thought to be particularly important in fast-changing environments, such as edges, providing an advantage for genetic diversity. Further investigation is needed to assess in greater detail how habitat loss affects O. chelifer biology. Our study is a first step toward elucidating edge effects on genetic diversity of ant colonies, a topic still poorly explored in tropical environments.
... Note that our individual-based simulations allow polymorphic sites to contribute to adaptation and hybrid breakdown and allow for transient overdominance, which is often found in Fisher's geometric model with diploids (e.g. [38]). For example, the fixation probability of a mutation can depend on the individual in which it arises in a polymorphic population, which is not true in models that simply track the series of fixed substitutions. ...
Genetic divergence among allopatric populations builds reproductive isolation over time. This process is accelerated when populations face a changing environment that allows large-effect mutational differences to accumulate, but abrupt change also places populations at risk of extinction. Here we use simulations of Fisher's geometric model with explicit population dynamics to explore the genetic changes that occur in the face of environmental changes. Because evolutionary rescue leads to the fixation of mutations whose phenotypic effects are larger on average compared with populations not at risk of extinction, these mutations are thus more likely to lead to reproductive isolation. We refer to the formation of new species from the ashes of populations in decline as the phoenix hypothesis of speciation. The phoenix hypothesis predicts more substantial hybrid fitness breakdown among populations surviving a higher extinction risk. The hypothesis was supported when many loci underlie adaptation. With only a small number of potential rescue mutations, however, mutations that fixed in different populations were more likely to be identical, with such parallel changes reducing isolation. Consequently, reproductive isolation builds fastest in populations subject to an intermediate extinction risk, given a limited number of mutations available for adaptation.
... Similar studies in asexual isogenic diploids have shown that ploidy can influence the dynamics of adaptation, with diploids often adapting more Linder et al. · https://doi.org/10.1093/molbev/msac248 MBE slowly than haploids, likely due to the effects of Haldane's sieve (Zeyl et al. 2003;Sellis et al. 2011Sellis et al. , 2016Gerstein et al. 2014;Fisher et al. 2018;Marad et al. 2018;Johnson et al. 2021). Diploids also appear to accumulate more potentially deleterious mutations (increased mutational load), and continue to adapt longer than haploids, likely due to the effects of mitotic recombination (Forche et al. 2011;Gerstein et al. 2014;Johnson et al. 2021). ...
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
