Biology subjects

Blanckaert, A.

Publications and source records attributed to Blanckaert, A..

9 recordsLinked to original sources

bioRxiv2026

The Joint Impact of Deleterious Mutations, Dominance, and Gene Flow on Linked Neutral Variation in Structured Populations

Most species are geographically structured, leaving characteristic signatures in neutral regions of the genome. These signatures can be distorted when neutral regions are linked to deleterious mutations. In such regions, purifying selection can reduce genetic diversity through Background Selection (BGS) or, for recessive mutations, increase diversity through Associative Overdominance (AOD). While the effect of BGS and AOD are well characterized in panmictic populations, their effects remain largely unexplored in structured populations. Here, we investigated an Isolation with Migration model using forward simulations across a range of migration, selection, dominance, and recombination parameters. We first used a genotype-based approach to quantify the effects of deleterious mutations on standard summary statistics ({pi}, dxy, FST, DAFi). We then showed that an Ancestral Recombination Graph-based (ARG) approach, tracking tree sequences from a sample of one diploid per deme, recovers the same patterns while directly relating genetic variation to the underlying coalescent processes. When recombination is sufficiently low, we found a BGS-driven regime for weakly codominant mutations, characterized by lower diversity and increased genetic differentiation (FST). For recessive mutations, we first identified an AOD-driven regime, characterized by increased diversity and lower FST values followed by a transition to a subsequent BGS-driven regime. Genealogies were similarly impacted by deleterious mutations: BGS shrunk coalescent times and produced a shift towards lineage sorting topologies, while AOD stretched coalescent times and produced a shift toward incomplete lineage-sorting topologies. These patterns were weakened by gene flow, with FST and topologies remaining close to expected under neutrality, while diversity and coalescence times remained robust to demography. Our results provide clear evidence of BGS, AOD, and of their transition in a structured model with gene flow. Importantly, these processes leave distinct and interpretable signatures on gene trees, highlighting the potential of ARG-based approaches for inferring linked selection and dominance in structured populations. Author summaryCharacterizing how demography and selection jointly shape genomic variation is a central question in population genetics. As deleterious mutations reduce fitness, they are continuously removed from populations by purifying selection. Through linkage, this affects nearby regions of the genome, leaving signatures of selection on linked neutral genetic diversity. While these effects are well understood in random mating populations, much less is known in structured populations. Specifically, the occurrence of Background Selection (BGS), which reduces diversity, and Associative Overdominance (AOD), which increases diversity, remains underexplored. Here, we used simulations to investigate how deleterious mutations shape genomic variation in a structured two-population isolation with migration model. By combining standard population genetic analyses with a genealogical approach based on Ancestral Recombination Graphs (ARGs), we showed that BGS and AOD leave distinct and interpretable signatures on common summary statistics and the underlying genealogies. We identified clear signatures of BGS and AOD when recombination was low and revealed a transition from AOD to BGS for recessive mutations, as the strength of selection increased. Our results highlight the importance of jointly considering demography and linked selection when interpreting genomic data and demonstrate the potential of ARGs to jointly infer demography, selection, and dominance from genomic data.

evolutionary biology↗

bioRxiv2025

Interactions between mechanisms of reproductive isolation

Speciation is responsible for the diversity of species observed today and corresponds to the build-up of reproductive isolation between populations. Reproductive isolation can be generated by different mechanisms that have been extensively characterized, yet how their interactions affect speciation remains largely unknown. Here, we explicitly model the interaction of three key mechanisms (local adaptation, mate choice and genetic hybrid incompatibilities) quantifying their relative contribution to the evolution of reproductive isolation. We modeled two populations exchanging migrants using Fishers Geometric Model for local adaptation, phenotype matching for mate choice, and multiple pairs of Bateson-Dobzhansky-Muller Incompatibilities (DMI). All three mechanisms were determined by the same set of loci, creating conditions for interactions between barriers both at the genetic and population levels. We found very few cases where the three barriers evolved together. Instead, two barriers could evolve depending on the migration rate: either local adaptation and genetic incompatibilities for limited migration, or local adaptation and mate choice for higher migration. Our results showed that local adaptation due to ecological differentiation was the first to evolve and by far the most effective reproductive barrier. Finally, we demonstrated that in a polygenic model, populations could become locally adapted and evolve strict mate choice, yet they would not accumulate incompatibilities provided that there was sufficient gene flow.

evolutionary biology↗

bioRxiv2023

In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation.

Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e., the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability.

evolutionary biology↗

bioRxiv2021

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

evolutionary biology↗

bioRxiv2020

The limits to parapatric speciation 3: Evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation.

Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky-Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that may initially face many incipient species. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation.

evolutionary biology↗

bioRxiv2019

Muller’s Ratchet and the Long-Term Fate of Chromosomal Inversions

Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion. Author SummaryA chromosomal inversion is a segment of the chromosome that is flipped (inverted arrangement) relative to the normal orientation (standard arrangement). Such structural mutations may facilitate evolutionary processes such as adaptation and speciation, because reduced recombination in inverted regions allows beneficial combinations of alleles to behave as a "single unit". This locally reduced recombination can have major consequences for the evolution of the allelic content inside the inversion. We used simulations to investigate some of these consequences. Inverted regions tended to accumulate more deleterious recessive mutations than the rest of the genome, which decreased the fitness of homokarotypes (individuals with two copies of the same arrangement). This led to a strong selective advantage for heterokaryotypes (individuals with one copy of each arrangement), maintaining the inversion polymorphism in the population. The accumulation of deleterious mutations also resulted in strong divergence between arrangements. We occasionally observed an arrangement that diverged into a small number of highly differentiated haplotypes, stopping the fitness decrease in homokaryotypes. Our results highlight the dynamic features of inversions by showing how the evolution of allelic content can greatly affect the fate of an inversion.

evolutionary biology↗

bioRxiv2018

The Limits to Parapatric Speciation II: Strengthening a Preexisting Genetic Barrier to Gene Flow in Parapatry

Parapatric speciation has recently received a lot of attention. By encompassing the whole continuum between allopatric and sympatric scenarios, it includes many potential scenarios for the evolution of new species. Building upon previous work, we investigate how a genetic barrier to gene flow, that relies on a single postzygotic genetic incompatibility, may further evolve. We consider a continent island model with three loci involved in pairwise Dobzhansky-Muller incompatibilities (DMIs). Using a deterministic and analytic approach, we derive the conditions for invasion of a new mutation and its consequences on an already existing genetic barrier to gene flow. We focus on quantifying the impact of the epistasis generated by the new mutation on the genetic barrier. We show that the accumulation of genetic incompatibilities in the presence of gene flow is a complex process, where new mutations can either strengthen or destroy a preexisting barrier. In particular, preexisting polymorphism and incompatibilities do not always facilitate the growth of the genetic barrier by accumulation of further barrier genes. Migration may disrupt the snowball effect (the accelerating rate of DMI accumulation in allopatry) because incompatibilities are directly tested by selection. Our results also show an ambiguous role of gene flow, which can either impede or facilitate the strengthening of the genetic barrier. Overall, our results illustrate how the inclusion of gene flow renders the building of a genetic barrier difficult to analyze.

genetics↗

bioRxiv2018

In search of the Goldilocks zone for hybrid speciation

Hybridization has recently gained considerable interest both as a unique window for observing speciation mechanisms and as a potential engine of speciation. The latter remains a controversial topic. It was recently hypothesized that the reciprocal sorting of genetic incompatibilities from parental species could result in hybrid speciation, when the hybrid population maintains a mixed combination of the parental incompatibilities that prevents further gene exchange with both parental populations. However, the specifics of the purging/sorting process of multiple incompatibilities have not been examined theoretically.\n\nWe here investigate the allele-frequency dynamics of an isolated hybrid population that results from a single hybridization event. Using models of 2 or 4 loci, we investigate the fate of one or two genetic incompatibilities of the Dobzhansky-Muller type (DMIs). We study how various parameters affect both the sorting/purging of the DMIs and the probability of observing hybrid speciation by reciprocal sorting. We find that the probability of hybrid speciation is strongly dependent on the linkage architecture (i.e. the order and recombination distance between loci along chromosomes), the population size of the hybrid population, and the initial relative contribution of the parental populations to the hybrid population. We identify a Goldilocks zone for specific linkage architectures and intermediate recombination rates, in which hybrid speciation becomes highly probable. Whereas an equal contribution of parental populations to the hybrid populations maximizes the hybrid speciation probability in the Goldilocks zone, other linkage architectures yield unintuitive asymmetric maxima. We provide an explanation for this pattern, and discuss our results both with respect to the best conditions for observing hybrid speciation in nature and their implications regarding patterns of introgression in hybrid zones.\n\nSummaryHybridization is observed ubiquitously in nature. Its outcome can range from extinction to the creation of new species. With respect to the latter, the probability of homoploid hybrid speciation, i.e. the formation of a new species as a result of an hybridization event without changes in the ploidy of the organism, is a hotly debated topic. Here, we analyze a minimal model for homoploid hybrid speciation, in which reproductive isolation is achieved by means of (postzygotic) Dobzhansky-Muller incompatibilities. When these postzygotic genetic incompatibilities are resolved in the hybrid population, their reciprocal sorting can result in reproductive isolation from both parental populations, thus creating a hybrid species. We show that, in accordance with the current literature, hybrid speciation tends to be rare. However, specific arrangements of the genes responsible for reproductive isolation can make reciprocal sorting almost unavoidable and thus create barriers to the parental population in an almost deterministic matter. We discuss the implications of these results for hybrid speciation and patterns of introgression in nature.

evolutionary biology↗

bioRxiv2017

Conflict between heterozygote advantage and hybridincompatibility in haplodiploids (and sex chromosomes)

In many diploid species the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Z chromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization. Here, hybrid females have increased survivorship but hybrid males are inviable. To understand how the unusual hybrid population may be maintained, we developed a mathematical model with hybrid incompatibility, female heterozygote advantage, recombination, and assortative mating. The rugged fitness landscape resulting from the co-occurrence of heterozygote advantage and hybrid incompatibility results in a sexual conflict in haplodiploids, which is caused by the ploidy difference. Thus, whereas heterozygote advantage always promotes long-term polymorphism in diploids, we find various outcomes in haplodiploids in which the population stabilizes either in favor of males, females, or via maximizing the number of introgressed individuals. We discuss these outcomes with respect to the potential long-term fate of the Finnish wood ant population, and provide approximations for the extension of the model to multiple incompatibilities. Moreover, we highlight the general implications of our results for speciation and hybridization in haplodiploids versus diploids, and how the described fitness relationships could contribute to the outstanding role of sex chromosomes as hotspots of sexual antagonism and genes involved in speciation.

evolutionary biology↗