Biology subjects

Roze, D.

Publications and source records attributed to Roze, D..

18 recordsLinked to original sources

bioRxiv2026

Self-fertilization reverses the direction of selection on recombination

The evolution of recombination is thought to be influenced by many factors, including the mating system. Here, we provide an experimental test of how self-fertilization (selfing) affects the evolution of a recombination modifier. We used experimental populations of Caenorhabditis elegans segregating for the recombination modifier rec-1, a mutant that redistributes crossovers from the genetically diverse chromosome arms toward the less diverse central regions. By evolving populations under varying selfing rates, we show that increasing selfing reverses selection acting on the rec-1 mutant, from positive to negative. Simulations show that this reversal can be explained by an expansion of the genomic region over which the modifier remains associated with the genetic combinations it creates. These results demonstrate that selfing can fundamentally alter the evolutionary fate of recombination modifiers and reveal a mechanism not predicted by previous theoretical models of recombination evolution under different mating systems, which assumed uniform recombination landscapes.

evolutionary biology↗

bioRxiv2026

Differential selection between sexes and the evolution of recombination in haplodiploids

Eusocial Hymenoptera present the highest known recombination rates among metazoans, which evolved several times independently among bees, ants and wasps. Several hypotheses have been proposed to explain this observation, including stronger selection for recombination caused by coevolving parasites and pathogens, and strong sexual selection among haploid males due to male-biased sex ratios among reproductive individuals. In this article, we explore the effects of haplodiploidy and differential selection between sexes on the evolution of recombination, by analyzing a three-locus model in which selection for recombination stems from negative epistasis between selected loci. Our analytical predictions are compared with the results of individual-based simulations in which deleterious mutations occur along a linear chromosome. Our results show that, at mutation-selection balance for deleterious alleles, increasing the strength of selection against deleterious alleles (due to the effect of male haploidy and/or sexual selection) tends to reduce selection for recombination. However, an increase in the overall magnitude of negative epistasis (which may also be due to male haploidy and/or sexual selection) combined with the fact that recombination only occurs in females may increase selection for recombination substantially. Our model also shows that, in conditions favoring recombination, increasing recombination in meioses leading to parthenogenetic ovules (and male offspring) may yield stronger benefits than in meioses leading to fertilized ovules (and female offspring).

evolutionary biology↗

bioRxiv2026

The causes of signed linkage disequilibrium within genomic datasets

The signed linkage disequilibrium (LD) among selected mutations plays an important role in theoretical models of the evolution of sex and recombination. Several recent studies have quantified LD among mutations in genomic datasets, often reporting positive LD, particularly among mutations presumed to be less deleterious, such as synonymous variants. In this article, we investigate two potential sources of this positive LD: the focus on rare alleles, as adopted in several previous studies, and errors arising in the mapping of short-read sequences onto a reference genome. Using coalescent simulations, we extend previous theoretical results of the effect of focusing on rare alleles, and show that derived neutral alleles present at similar frequencies tend to be in positive LD, while alleles present at different frequencies tend to be in negative LD. Reanalyzing datasets from Capsella grandiflora and Drosophila melanogaster, we show that LD among synonymous derived alleles vanishes in the absence of any conditioning on frequency, while LD between mutations categorized as potentially deleterious by the SIFT4G program stays positive. However, we show that in both cases, this positive LD may be at least partly caused by the potential mismapping of a small fraction of sequences in some individuals, which could be a consequence of structural variants that are absent from the reference genome. Overall, these results show that average signed LD among mutations can be strongly affected by technical artifacts even if these concern only a minority of variants. Finally, we discuss other possible sources of positive LD among deleterious mutations.

genomics↗

bioRxiv2025

Effects of deleterious mutations on the fixation of chromosomal inversions on autosomes and sex chromosomes

Deleterious mutations have multiple effects on the fate of chromosomal inversions. In this article, we use individual-based simulations to estimate the fixation probabilities of neutral inversions under a constant input of deleterious mutations. As shown previously, we find that lucky inversions carrying a lower-than-average mutation load are initially favored and tend to selectively spread. Our results also outline the importance of Mullers ratchet caused by the absence of recombination in Y-linked and in rare autosomal inversions, reducing their fixation probabilities. Despite the fact that Y-linked inversions are more susceptible to Mullers ratchet, they can more easily fix than autosomal inversions despite initially carrying mutations, when these mutations have sufficiently low selection or dominance coefficients (sheltering effect). Similarly, the sheltering of deleterious alleles can increase the fixation probability of inversions capturing a mating-type locus, particularly under intermediate rates of self-fertilization. Overall, our results confirm that when mating is random and for realistic parameter values, the presence of deleterious alleles reduces the average fixation probability of autosomal, sex-linked or mating type-linked inversions below that of a neutral mutation. Nevertheless, the occasional fixation of a lucky inversion may have important macroevolutionary consequences, potentially contributing to the evolution of recombination arrest on sex chromosomes.

evolutionary biology↗

bioRxiv2025

Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing

The effect of natural selection on linked sites has been suggested to be a major determinant of genetic diversity. While it is in principle possible to estimate this effect from genome sequence data, interactions between selection, demography and inbreeding are expected to make inference less reliable. Here we investigate whether the genome-wide reduction in diversity due to background selection ([B]) can be accurately estimated when populations are at demographic non-equilibrium and/or reproduce by partial self-fertilisation. We show that the classic-BGS model is surprisingly robust to both demographic non-equilibrium and low rates of selfing, although both processes do lead to biased estimation of the distribution of fitness effects (DFE) of deleterious mutations. A high rate of selfing leads to poor estimation of both[B] and DFE parameters. We propose an alternative inference approach where background selection, demography and partial selfing are jointly estimated from windowed site frequency spectra. This approach, while approximate in nature, resolves most of the bias observed under the classic-BGS model and can also generate estimates of past demography that account for the effect of background selection and partial selfing. We apply the approach to genome sequence data from Capsella grandiflora and C. orientalis, which have contrasting mating systems and display a forty-fold difference in nucleotide diversity. Our results suggest that background selection has a weak effect on levels of genetic diversity in the outcrosser C. grandiflora ([B] = 0.89) and a more substantial effect in the predominantly selfing species C. orientalis ([B] = 0.44), but that background selection alone cannot explain their disparity in genetic diversity.

evolutionary biology↗

bioRxiv2025

Deleterious mutations and selection for sex in spatially structured, diploid populations

By increasing local genetic drift and generating inbreeding, population spatial structure may have important effects on the evolutionary benefits of sexual reproduction. In this article, we consider a population structured according to the island model, and use two and three-locus analytical models and multilocus simulations to explore the selective forces acting on a modifier locus affecting the rate of sexual reproduction of facultatively sexual organisms, in the presence of recurrent deleterious mutations. The results show that population structure and selection combine to generate a local excess of heterozygotes at selected loci (negative FIS), for both partially recessive and partially dominant deleterious alleles. The linkage disequilibrium between deleterious alleles may be either negative or positive depending on their dominance coefficient, the degree of population structure and the rate of sex. These genetic associations combine with many other ones to generate indirect selection at the sex modifier locus, generally favoring intermediate rates of sex even when sex entails direct fitness costs. Multilocus simulations show that the equilibrium rate of sex increases moderately as the degree of population structure increases. However, population structure may also prevent the irreversible spread of asexual mutants when the cost of sex is strong.

evolutionary biology↗

bioRxiv2024

Selection can favor a recombination landscape that limits polygenic adaptation

Meiotic crossover positions are uneven along eukaryotic chromosomes, giving rise to heterogeneous recombination rate landscapes. Genetic modifiers of local and genome-wide crossover positions have been described, but the selective pressures acting on them and their potential effect on adaptation in already-recombining populations remain unclear. We performed experimental evolution using a mutant that modifies the position of crossovers along chromosomes in the nematode Caenorhabditis elegans, without any detectable direct fitness effect. Our results show that when the recombination landscape is fixed, adaptation is facilitated by the modifier allele that, on average, increases recombination rates in genomic regions containing heritable fitness variation. However, in polymorphic populations containing both the wild-type and mutant modifier alleles, the allele that facilitates adaptation tends to decrease in frequency. This is likely because the allele that reduces recombination between selected loci at the genome-wide scale increases recombination in its chromosomal vicinity, and may thus benefit from local associations it establishes with beneficial genotype combinations. These results demonstrate that indirect selection acting on a recombination modifier mainly depends on its local effect, which may be decoupled from its consequences on genome-wide polygenic adaptation.

evolutionary biology↗

bioRxiv2024

Transient evolutionary epidemiology of viral adaptation and lethal mutagenesis

Beneficial mutations drive the within-host adaptation of viral populations and can prolong the duration of host infection. Yet, most mutations are not adaptive and the increase of the mean fitness of viral populations is hampered by deleterious and lethal mutations. Because of this ambivalent role of mutations, it is unclear if a higher mutation rate boosts or slows down viral adaptation. Here we study the interplay between selection, mutation, genetic drift and within-host dynamics of viral populations. We obtain good approximations for the transient evolutionary epidemiology of viral adaptation under the assumption that the mutation rate is high and the effects of non-lethal mutations remain small. We use this theoretical framework to discuss the feasibility of lethal mutagenesis to treat viral infections in the light of quantitative predictions we obtained for the critical mutation rates of a range of different viruses.

evolutionary biology↗

bioRxiv2024

A single theory for the evolution of sex chromosomes and the two rules of speciation

Sex chromosomes are involved in three major empirical patterns: Y (or W) chromosomes are often non-recombining and degenerate; heterogametic offspring (XY or ZW) from interspecific crosses are more often sterile or inviable than homogametic offspring (Haldanes rule); the X (or Z) has a disproportionately large effect on reproductive isolation between species compared to autosomes (the large X effect). Each observation has received its own tailored explanation involving multiple genetic and evolutionary causes. Here, we show that these empirical patterns all emerge from a single theory for sex chromosome evolution incorporating the co-evolution of cis and trans-acting regulators of gene expression, and leading to systematic misexpression of dosage-compensated genes in heterogametic F1 hybrids, for both young and old sex chromosomes. Structured AbstractO_ST_ABSIntroductionC_ST_ABSSex chromosomes have long been known to play a prominent role in the genetics of speciation, captured by the famous "two rules of speciation". The first, attributed to J.B.S. Haldane and known as Haldanes rule, corresponds to the general observation that when, among interspecific hybrids, one sex is inviable or sterile, it is more often the heterogametic sex (XY or ZW). The second is known as the large X effect, and refers to the fact that the X or Z chromosome often has a stronger effect on hybrid fitness than autosomes of equivalent size. While several theories have been proposed to explain these empirical patterns, none has been able to account for all the observations, leading to the current consensus that the two rules of speciation may have multiple causes. Furthermore, these theories remain disconnected from general models predicting sex chromosome evolution. RationaleWe have recently developed a new theory for the evolution of sex chromosomes, showing that the coevolution of cis and trans regulators of gene expression can lead to stable recombination arrest between the X and Y (or Z and W) chromosomes, degeneration of the Y (or W) chromosome and dosage compensation. Here we investigate the role of sex chromosomes on the fitness of interspecific hybrids under this general model, considering different scenarios that correspond to different stages in the evolution of sex chromosomes. We also investigate the effect of genes with sex-specific effects that affect either male or female fertility. ResultsHaldanes rule and the large X effect are observed in all scenarios considered. Our model also captures "Darwins corollary" to Haldanes rule, i.e. an asymmetry between the effects of reciprocal crosses between species. These results are caused by the divergence of regulators of gene expression between species, due to the presence of a non-recombining, degenerate stratum on the Y chromosome either shared by both species or present in only one of them. In both cases, Haldanes rule results from the heterogametic sex inheriting X chromosome cis regulators from only one parental species that have not coevolved with the trans regulators of the other species, resulting in under or overexpression of dosage-compensated genes on the X (or Z) chromosome. While this regulatory divergence may be limited in the case of species with a global (chromosome-wide) somatic system of dosage compensation, regulatory divergence of germline-expressed genes may generate Haldanes rule for fertility in these species. Genes whose effect is restricted to the heterogametic sex often have strong effects on reproductive isolation and on the fitness of heterogametic hybrids, especially if they are silenced on the X (or Z) chromosome of one parental species and on the Y (or W) chromosome of the other. ConclusionOur study shows that a simple model of coevolution between cis and trans regulators of gene expression on sex chromosomes can explain the evolution of non-recombining, degenerate and dosage compensated Y and W chromosomes, Haldanes rule and the large X effect. It may also explain why Haldanes rule is based on viability is some taxa and on fertility in others, an observation that remained difficult to explain from previous theories. These results match with recent observations on the role of misregulation of gene expression on hybrid fitness, and open new perspectives of empirical research on the genetics of speciation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/585601v4_figa1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@e94472org.highwire.dtl.DTLVardef@8cbecaorg.highwire.dtl.DTLVardef@41cc5dorg.highwire.dtl.DTLVardef@1d00ea0_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSummary figure.C_FLOATNO A multilocus, individual-based simulation model was used to investigate the joint evolution of sex chromosomes and reproductive isolation between species. It includes deleterious mutations, mutations suppressing or restoring recombination and mutations affecting the strength of cis and trans regulators of gene expression. This model predicts the major features of sex chromosome evolution and the "two rules of speciation" (Haldanes rule and the large X effect). C_FIG

evolutionary biology↗

bioRxiv2023

Revisiting the shelter theory: can deleterious mutations alone explain the evolution of sex chromosomes?

Y and W chromosomes often stop recombining and degenerate. Most work on recombination suppression has focused on the mechanisms favoring recombination arrest in the short term. Yet, the long-term maintenance of recombination suppression is critical to evolving degenerate sex chromosomes. This long-term maintenance has been little investigated. In the long term, recombination suppression may be maintained for selective reasons (e.g., involving the emergence of nascent dosage compensation), or due to mechanistic constraints preventing the reestablishment of recombination, for instance when complex chromosomal rearrangements evolve on the Y. In this paper, we investigate these constraint theories. We show that they face a series of theoretical difficulties: they are not robust to extremely low rates of recombination restoration; they would rather cause population extinction than Y degeneration; they are less efficient at producing a non-recombining and degenerate Y than scenarios adding a selective pressure against recombination, whatever the rate of recombination restoration. Finally, whether such very high constraints exist is questionable. Very low rates of recombination reestablishment are sufficient to prevent Y degeneration, given the large fitness advantage to recover a non-degenerate Y or W for the heterogametic sex. The assumption of a lack of genetic variation to restore recombination seems also implausible given known mechanisms to restore a recombining pair of sex chromosomes.

evolutionary biology↗

bioRxiv2022

Causes and consequences of linkage disequilibrium among transposable elements within eukaryotic genomes

Sex and recombination can affect the dynamics of transposable elements (TEs) in various ways: while sex is expected to help TEs to spread within populations, the deleterious effect of ectopic recombination among transposons represents a possible source of purifying selection limiting their number. Furthermore, recombination may also increase the efficiency of selection against TEs by reducing selective interference among loci. In order to better understand the effects of recombination and reproductive systems on TE dynamics, this article provides analytical expressions for the linkage disequilibrium (LD) among TEs in a classical model in which TE number is stabilized by synergistic purifying selection. The results show that positive LD is predicted in infinite populations despite negative epistasis, due to the effect of the transposition process. Positive LD may substantial inflate the variance in the number of elements per genome in the case of partially selfing or partially clonal populations. Finite population size tends to generate negative LD (Hill-Robertson effect), the relative importance of this effect increasing with the degree of linkage among loci. The model is then extended in order to explore how TEs may affect selection for recombination. While positive LD generated by transposition generally disfavors recombination, the Hill-Robertson effect may represent a non-negligible source of indirect selection for recombination when TEs are abundant. However, the direct fitness cost imposed by ectopic recombination among elements generally drives the population towards low-recombination regimes, at which TEs cannot be maintained at a stable equilibrium.

evolutionary biology↗

bioRxiv2022

The evolution of recombination in self-fertilizing organisms

Cytological data from flowering plants suggest that the evolution of recombination rates is affected by the mating system of organisms, as higher chiasma frequencies are often observed in self-fertilizing species compared with their outcrossing relatives. Understanding the evolutionary cause of this effect is of particular interest, as it may shed light on the selective forces favoring recombination in natural populations. While previous models showed that inbreeding may have important effects on selection for recombination, existing analytical treatments are restricted to the case of loosely linked loci and weak selfing rates, and ignore the effect of genetic interference (Hill-Robertson effect), known to be an important component of selection for recombination in randomly mating populations. In this article, we derive general expressions quantifying the stochastic and deterministic components of selection acting on a mutation affecting the genetic map length of a whole chromosome along which deleterious mutations occur, valid for arbitrary selfing rates. The results show that selfing generally increases selection for recombination caused by interference among mutations as long as selection against deleterious alleles is sufficiently weak. While interference is often the main driver of selection for recombination under tight linkage or high selfing rates, deterministic effects can play a stronger role under intermediate selfing rates and high recombination, selecting against recombination in the absence of epistasis, but favoring recombination when epistasis is negative. Individual-based simulation results indicate that our analytical model often provides accurate predictions for the strength of selection on recombination under partial selfing.

evolutionary biology↗

bioRxiv2021

Y recombination arrest and degeneration in the absence of sexual dimorphism

Current theory proposes degenerated sex chromosomes evolve via three successive steps: recombination arrest, which links male-beneficial alleles to the Y chromosome; degeneration of these regions due to the inefficacy of natural selection in the absence of recombination; and lastly, the evolution of dosage compensation to correct the resulting low expression of X-linked genes in males. Here we investigate new models of sex chromosome evolution incorporating the coevolution of cis- and trans-regulators of gene expression. We show that the early emergence of dosage compensation favors the maintenance of Y-linked inversions by creating sex-antagonistic regulatory effects. This is followed by inversion degeneration caused by regulatory divergence between the X and Y chromosomes. In stark contrast to the current theory, the whole process occurs without any selective pressure related to sexual dimorphism. One Sentence SummaryTurning sex chromosome theory on its head: early evolution of dosage compensation can maintain successively forming Y chromosome strata that undergo genetic degeneration.

evolutionary biology↗

bioRxiv2019

The Geometry and Genetics of Hybridization

We develop an analytical framework for predicting the fitness of hybrid genotypes, based on Fishers geometric model. We first show that all of the model parameters have a simple geometrical and biological interpretation. Hybrid fitness decomposes into intrinsic effects of hybridity and heterozygosity, and extrinsic measures of the (local) adaptedness of the parental lines; and all of these correspond to distances in a phenotypic space. We also show how these quantities change over the course of divergence, with convergence to a characteristic pattern of intrinsic isolation. Using individual-based simulations, we then show that the predictions apply to a wide range of population genetic regimes, and divergence conditions, including allopatry and parapatry, local adaptation and drift. We next connect our results to the quantitative genetics of line crosses in variable or patchy environments. This relates the geometrical distances to quantities that can be estimated from cross data, and provides a simple interpretation of the "composite effects" in the quantitative genetics partition. Finally, we develop extensions to the model, involving selectively-induced disequilibria, and variable phenotypic dominance. The geometry of fitness landscapes provides a unifying framework for understanding speciation, and wider patterns of hybrid fitness.

evolutionary biology↗

bioRxiv2019

Epistasis, inbreeding depression and the evolution of self-fertilization

Inbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may also generate an advantage to selfers in terms of more efficient purging, while the effects of epistasis among those alleles on inbreeding depression and mating system evolution remain little explored. In this paper, we use a general model of selection to disentangle the effects of different forms of epistasis (additive-by-additive, additive-by-dominance and dominance-by-dominance) on inbreeding depression and on the strength of selection for selfing. Models with fixed epistasis across loci, and models of stabilizing selection acting on quantitative traits (generating distributions of epistasis) are considered as special cases. Besides its effects on inbreeding depression, epistasis may increase the purging advantage associated with selfing (when it is negative on average), while the variance in epistasis favors selfing through the generation of linkage disequilibria that increase mean fitness. Approximations for the strengths of these effects are derived, and compared with individual-based simulation results.

evolutionary biology↗

bioRxiv2019

Evolution of life cycles and reproductive traits: insights from 1 the brown algae

Brown algae are characterized by a remarkable diversity of life cycles, sexual systems, and reproductive modes, and these traits seem to be very labile across the whole group. This diversity makes them ideal models to test existing theories on the evolution of alternation between generations, and to examine correlations between life cycle and reproductive life history traits. In this study, we investigate the dynamics of trait evolution for four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assign states to up to 70 species in a multi-gene phylogeny of brown algae, and use maximum likelihood and Bayesian analyses of correlated evolution, taking phylogeny into account, to test for correlations between life history traits and sexual systems, and to investigate the sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth may evolve because it allows the complementation of deleterious mutations, and that haploid sex determination is ancestral in relation to diploid sex determination. However, the idea that increased zygotic and diploid growth is associated with increased sexual dimorphism is not supported by our analysis. Finally, it appears that in the brown algae isogamous species evolved from anisogamous ancestors.

evolutionary biology↗

bioRxiv2018

Asexual reproduction drives the reduction of transposable element load

Theory predicts that sexual reproduction can both facilitate and restrain transposable element (TE) accumulation by providing TEs with a means of spreading to all individuals in a population and facilitating TE load reduction via purifying selection. By quantifying genomic TE loads over time in experimental sexual and asexual Saccharomyces cerevisiae populations, we provide direct evidence that asexual reproduction drives a reduction of TE loads. We show, using simulations, that this reduction occurs via evolution of TE activity, most likely via increased excision rates. Thus, sex is a major driver of genomic TE loads and at the root of the success of TEs.

evolutionary biology↗

bioRxiv2017

Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection

The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic variance Vg, mutation load L and inbreeding depression{delta} under stabilizing selection acting on a arbitrary number n of quantitative traits coded by biallelic loci with additive effects. Overall, our model predicts a decrease in the equilibrium genetic variance with increasing selfing rates; however, the relationship between self-fertilization and the variables of interest depends on the strength of associations between loci, and three different regimes are observed. When the U/n ratio is low (where U is the total haploid mutation rate on selected traits) and effective recombination rates are sufficiently high, genetic associations between loci are negligible and the genetic variance, mutation load and inbreeding depression are well predicted by approximations based on single-locus models. For higher values of U/n and/or lower effective recombination, moderate genetic associations generated by epistasis tend to increase Vg, L and{delta} , this regime being well predicted by approximations including the effects of pairwise associations between loci. For yet higher values of U/n and/or lower effective recombination, a different regime is reached under which the maintenance of coadapted gene complexes reduces Vg, L and{delta} . Simulations indicate that the values of Vg, L and{delta} are little affected by assumptions regarding the number of possible alleles per locus.

evolutionary biology↗