Biology subjects

Veber, A.

Publications and source records attributed to Veber, A..

7 recordsLinked to original sources

bioRxiv2026

The fate of mutations on Y chromosomes andautosomes: a unified Wright-Fisher frameworkaccounting for segregation time

Understanding how mutations evolve on Y chromosomes is central to explaining the origin, diversity and persistence of sex chromosomes. Mutations occurring on the Y chromosome in sexual populations experience selective dynamics that differ markedly from those on autosomes, due to a reduced effective population size and the presence of large non-recombining regions containing alleles maintained in a permanently heterozygous state. These specific features alter gene transmission in the Y chromosome population compared to autosomes, even within the same pedigree. Here, we provide a two-sex diploid Wright-Fisher model that explicitly incorporates both sex chromosomes and autosomes within a unified population framework, in order to capture the influence of these specificities on the fate of mutations, not only considering fixation probabilities but also segregation times. We use diffusion approximations and provide analytical and numerical tools to compute these quantities across a wide range of parameters and selection regimes. We recover classical results on fixation probabilities in various scenarios, including purely beneficial, deleterious or overdominant mutations, and extend them in the light of mean segregation time, a key but often overlooked determinant of evolutionary outcomes over finite timescales. In particular, our analyses show that overdominant mutations are overall more likely to fix in observable time windows on the Y chromosome than on autosomes. Individual-based simulations corroborate our approximations and highlight parameter regimes where the theoretical approach is particularly useful, especially for parameter values inducing long segregation times or small fixation probabilities, for which simulations are impractical. Our results provide a comprehensive and tractable framework for clarifying how chromosome-specific features shape evolutionary dynamics beyond fixation probabilities alone.

evolutionary biology↗

bioRxiv2025

Stepwise expansion of recombination suppression on sex chromosomes and other supergenes through lower load advantage and deleterious mutation sheltering

Many organisms possess sex chromosomes with non-recombining regions that have expanded progressively. Yet, the causes of this stepwise expansion remain poorly understood. Here, using mathematical modeling and stochastic simulations, we show that the widespread presence of deleterious recessive mutations in genomes can generate several phenomena that can contribute to the evolution of recombination suppression on sex chromosomes. We demonstrate that a significant proportion of new chromosomal inversions, or any other recombination suppressor, are initially advantageous because they carry fewer mutations than average. However, these less-loaded inversions generally fail to fix on autosomes because, as their frequency increases, the recessive deleterious mutations they carry are more likely to occur in a homozygous state, leading to a selective disadvantage. In contrast, the permanent heterozygosity of Y-like sex chromosomes shelters their inversions from this disadvantage, facilitating their fixation and thereby the stepwise expansion of non-recombining regions. Due to this sheltering effect, we show that fixation probabilities are substantially higher on Y-like chromosomes than on autosomes across a wide range of parameters, particularly when segregating deleterious mutations are moderately to strongly recessive, and this is true even after controlling for differences in effective population sizes between those chromosomes. Then, once recombination is suppressed, deleterious mutations accumulate on inversions, which could select for recombination restoration. However, we show that the accumulation of overlapping genomic rearrangements following recombination suppression can prevent its restoration. Overall, our theoretical model proposes a testable framework that may contribute to explaining evolutionary strata on sex and mating-type chromosomes, and other supergenes.

evolutionary biology↗

bioRxiv2024

Deleterious mutations can contribute to the evolution of recombination suppression between sex chromosomes

Many organisms have sex chromosomes with large non-recombining regions that expand in a stepwise manner, although the underlying reasons remain poorly understood. Recently, we proposed that recombination suppression may evolve in sex chromosomes simply because of the presence of recessive deleterious mutations within genomes. Specifically, we demonstrated that chromosomal inversions suppressing recombination and carrying by chance fewer deleterious mutations than average have a selective advantage. In addition, we showed that the permanent heterozygosity of Y-like sex chromosomes facilitates the fixation of these less-loaded inversions by a sheltering effect, i.e., by preventing the expression of recessive deleterious mutations in a homozygous state when they increase in frequency. In contrast, similar less-loaded inversions in autosomes suffer from a disadvantage in the homozygous state as their frequency increases, preventing their fixation. However, the methodology and significance of our previous study have been questioned. Here, we present new analyses that further reinforce our original claims, demonstrating that the lower-load advantage and the sheltering effect can explain the fixation of inversions on sex chromosomes over a broad range of parameter values. We show that these mechanisms promote the fixation of inversions on Y-like chromosomes at rates exceeding those expected under drift alone. We used, as a control, autosomes with a similar population size as the Y chromosome, which, we argue, provides the appropriate neutral control for the sheltering effect. We also address criticisms regarding our focus on inversions surviving the first 20 generations in a figure of our previous study, and show that these criticisms stemmed from a misunderstanding of what this figure was intended to illustrate. Including all inversions, even those that went extinct within 20 generations, does not alter our conclusions. Overall, the present study offers new support for our theory based on the combination of lower-load advantage and sheltering effect, and addresses the questions about its significance and range of applicability.

evolutionary biology↗

bioRxiv2022

Drosophilid cuticle pigmentation impacts body temperature

Cuticle pigmentation has been clearly demonstrated to impact body temperature for several relatively large species of insects, but it was questioned for small insects. Here we used a thermal camera to assess the impact of drosophilid cuticle pigmentation on body temperature when individuals are exposed to light. We compared mutants of large effects within species (Drosophila melanogaster ebony and yellow mutants). Then we analyzed the impact of naturally occurring pigmentation variation within species complexes (Drosophila americana/Drosophila novamexicana and Drosophila yakuba/Drosophila santomea). Finally we analyzed lines of D. melanogaster with moderate differences in pigmentation. We found significant differences in temperatures for each of the four pairs we analyzed. The temperature differences appeared to be proportional to the differently pigmented area: between Drosophila melanogaster ebony and yellow mutants or between Drosophila americana and Drosophila novamexicana, for which the whole body is differently pigmented, the difference in temperatures was around 0.6{degrees}C {+/-}0.2{degrees}C. By contrast, between D. yakuba and D. santomea or between Drosophila melanogaster Dark and Pale lines, for which only the posterior abdomen is differentially pigmented, we detected a temperature difference of about 0.14{degrees}C {+/-}0.10{degrees}C. This demonstrates that cuticle pigmentation has ecological implications in drosophilids regarding adaptation to environmental temperature.

evolutionary biology↗

bioRxiv2022

The fate of recessive deleterious or overdominant mutations near mating-type loci under partial selfing

Large regions of suppressed recombination having extended over time occur in many organisms around genes involved in mating compatibility (sex-determining or mating-type genes). The sheltering of deleterious alleles has been proposed to be involved in such expansions. However, the dynamics of deleterious mutations partially linked to genes involved in mating compatibility are not well understood, especially in finite populations. In particular, under what conditions deleterious mutations are likely to be maintained for long enough near mating-compatibility genes remains to be evaluated, especially under selfing, which generally increases the purging rate of deleterious mutations. Using a branching process approximation, we studied the fate of a new deleterious or overdominant mutation in a diploid population, considering a locus carrying two permanently heterozygous mating-type alleles, and a partially linked locus at which the mutation appears. We obtained analytical and numerical results on the probability and purging time of the new mutation. We investigated the impact of recombination between the two loci and of the mating system (outcrossing, intra and inter-tetrad selfing) on the maintenance of the mutation. We found that the presence of a fungal-like mating-type locus (i.e. not preventing diploid selfing) always sheltered the mutation under selfing, i.e. it decreased the purging probability and increased the purging time of the mutations. The sheltering effect was higher in case of automixis (intra-tetrad selfing). This may contribute to explain why evolutionary strata of recombination suppression near the mating-type locus are found mostly in automictic (pseudo-homothallic) fungi. We also showed that rare events of deleterious mutation maintenance during strikingly long evolutionary times could occur, suggesting that deleterious mutations can indeed accumulate near the mating-type locus over evolutionary time scales. In conclusion, our results show that, although selfing purges deleterious mutations, these mutations can be maintained for very long times near a mating-type locus, which may contribute to promote the evolution of recombination suppression in sex-related chromosomes.

evolutionary biology↗

bioRxiv2019

Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees

The large state space of gene genealogies is a major hurdle for inference methods based on Kingmans coalescent. Here, we present a new Bayesian approach for inferring past population sizes which relies on a lower resolution coalescent process we refer to as \"Tajimas coalescent\". Tajimas coalescent has a drastically smaller state space, and hence it is a computationally more efficient model, than the standard Kingman coalescent. We provide a new algorithm for efficient and exact likelihood calculations for data without recombination, which exploits a directed acyclic graph and a correspondingly tailored Markov Chain Monte Carlo method. We compare the performance of our Bayesian Estimation of population size changes by Sampling Tajimas Trees (BESTT) with a popular implementation of coalescent-based inference in BEAST using simulated data and human data. We empirically demonstrate that BESTT can accurately infer effective population sizes, and it further provides an efficient alternative to the Kingmans coalescent. The algorithms described here are implemented in the R package phylodyn, which is available for download at https://github.com/JuliaPalacios/phylodyn.

genetics↗

bioRxiv2017

Full likelihood inference from the site frequency spectrum based on the optimal tree resolution

We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated. We assume that the population may have demographically changed and may be non-panmictically structured, as reflected by the branch lengths and the topology of the genealogical tree of the sample, respectively. We also assume that mutations conform to the infinitely-many-sites model. We achieve this by a controlled Markov process that generates particles in the hidden space of SFS histories which are always compatible with the observed SFS.\n\nTo produce the particles, we use Aldous Beta-splitting model for a one parameter family of prior distributions over genealogical topologies or shapes (including that of the Kingman coalescent) and allow the branch lengths or epoch times to have a parametric family of priors specified by a model of demography (including exponential growth and bottleneck models). Assuming independence across unlinked loci, we can estimate the likelihood of a population scenario based on a large collection of independent SFS by an importance sampling scheme, using the (unconditional) distribution of the genealogies under this scenario when the latter is available. When it is not available, we instead compute the joint likelihood of the tree balance parameter {beta} assuming that the tree topology follows Aldous Beta-splitting model, and of the demographic scenario determining the distribution of the inter-coalescence times or epoch times in the genealogy of a sample, in order to at least distinguish different equivalence classes of population scenarios leading to different tree balances and epoch times. Simulation studies are conducted to demonstrate the capabilities of the approach with publicly available code.

genetics↗