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Peischl, S.

Publications and source records attributed to Peischl, S..

At least 19 recordsLinked to original sources

Environmental gradients and the establishment of chromosomal inversions

Chromosomal inversions are thought to promote local adaptation by capturing combinations of locally beneficial alleles and shielding them from recombination. Many of the best-documented examples are inversions that form clines along environmental gradients, yet analytical theory for this mechanism has remained confined to continent-island and two-deme models. We combine classical cline theory with quasi-linkage equilibrium approximations and spatial branching processes to derive the growth rate, establishment probability, and total establishment rate of a rare inversion along continuous environmental gradients of varying shape. After rescaling space by the characteristic cline width, all three quantities follow universal profiles and simple scaling laws. At a sharp environmental transition, the local growth rate of an inversion equals the selection acting on the captured alleles, independently of dispersal. Yet its establishment probability is only about one tenth of that value, again independently of dispersal, because a founding lineage disperses over the same spatial scale on which its fitness changes. In contrast to two-deme models, where the total establishment rate peaks at intermediate migration, along a cline it increases monotonically with dispersal, as successful inversions originate over an increasingly broad region on the flanks of the cline. Because the local growth rate depends only on the resident single-locus clines and the dispersal rate, the potential for inversion establishment can be estimated from observable allele-frequency clines without knowledge of the underlying fitness landscape. Stochastic simulations confirm these predictions. Our results provide a quantitative link between clinal patterns of genetic variation and the evolution of chromosomal inversions.

evolutionary biology↗

Heterogeneous evolution of effective recombination landscapes across percomorph fishes

Recombination shapes allelic combinations across the genome and plays a central role in adaptation and speciation. While recombination rates are known to vary and evolve, how recombination landscapes diverge between populations and which processes drive this divergence remains poorly understood. Here, we use the Population Recombination Divergence Index (PRDI) to quantify divergence in effective recombination landscapes between seven pairs of populations and species from four percomorph fish lineages (cichlids, sticklebacks, killifish, and clownfish). While accounting for stochasticity and confounders of linkage disequilibrium (LD) -based recombination rate estimates, we find that recombination landscapes diverged substantially in all comparisons. This divergence generally increases with genetic differentiation and divergence time, but the amount of PRDI accumulated per unit of genetic divergence (FST), net nucleotide divergence (da), or divergence time varies markedly among population and species pairs. Comparisons across systems suggest that PRDI accumulation tends to be faster (per unit of FST, da, or divergence time) in pairs with higher inferred gene flow. We also introduce a local version of PRDI (_l) to better characterize genomic heterogeneity in effective recombination divergence. We find that higher inferred gene flow between populations tends to be associated with stronger intragenomic correlation between local FST and _l. Finally, we propose a conceptual framework for investigating how divergent selection and gene flow may interact to shape effective recombination landscape divergence. Our work highlights the heterogeneous dynamics of effective recombination landscape evolution, and motivates further theoretical and empirical efforts to integrate recombination landscape evolution into studies of adaptation and speciation.

evolutionary biology↗

The influence of incompatibilities and heterosis on hybrid population genetics

A long-standing question in evolutionary biology is: Under what circumstances can speciation occur despite hybridisation or because of hybridisation? Some models of hybrid incompatibilities predict that speciation can occur even in the presence of gene flow and strong selection against hybrids, an outcome also influenced by genetic contributions from parental species and genetic architecture. On the other hand, empirical work has shown that heterosis can counteract the effect of incompatibilities, hindering the speciation process. Theoretical models that simultaneously consider the positive and negative impacts of hybridisation on fitness remain scarce, raising questions about the effects of hybrid incompatibilities in the presence of heterosis. To address this question, we study how (Bateson)-Dobzhansky-Muller incompatibilities (BDMIs) interact with overdominant mutations in a two-locus population genetics model of an isolated hybrid population. We find that the strength of overdominance relative to incompatibilities determines the long-term genetic composition of the hybrid population. We show that high recombination exposes incompatibilities to selection and reduces the frequency of derived alleles in the hybrid population, limiting the strength of BDMIs that can be maintained by the balance with overdominance. We also show how neutral variation is affected by the strength of selection and the recombination rate between incompatible loci, generating patterns that include an increase in local variation resembling associative overdominance, or a reduction resembling background selection. Such variation of neutral variation, particularly at intermediate distances from BDMI loci, can generate peaks or troughs of diversity that are explained by the recombination rate between BDMI loci, and initial proportions of admixture between parental populations. Our work demonstrates how the genomic conflict caused by the interplay of overdominance and hybrid incompatibilities, recombination, and parental contributions, shape the genome of an isolated hybrid population.

evolutionary biology↗

Recombination on 'non-recombining' sex chromosomes: empirical insights from the blackspotted stickleback

One hallmark of sex chromosome evolution is recombination suppression driven by inversions. The resulting non-recombining sex-linked regions accumulate deleterious mutations and functionally degenerate. The question therefore arises: why does selection not favor the reestablishment of recombination? Two (non-exclusive) explanations for this have been proposed: 1) selection to maintain linkage between the Primary Sex Determination Locus (PSDL) and sexually antagonistic loci - loci with alleles that are beneficial to one sex but detrimental to the other; and 2) the rarity of reversions - structural mutations that reverse the inversion that initially suppressed recombination. Empirical perspectives are sorely needed to evaluate the relevance of these models. Here, we characterised the intermediate stages of sex chromosome evolution in the blackspotted stickleback (Gasterosteus wheatlandi). We generated high-quality, phased assemblies and annotations for the X and Y chromosomes, as well as population-level sequencing. Using these data, we inferred distinct recombination loss events and their associated inversions. Most significantly, we find support from multiple lines of evidence for a [~]2 Mb recombination event that likely occurred via double crossover within an existing non-recombining inversion. This result highlights that rare recombination can occur within sex-linked inversions. Simulations suggest that such histories of gene flux may allow for a novel empirical framework, adapted from work on autosomal inversions, to infer evolutionary processes at work within sex-linked non-recombining regions and distinguish between models to explain the maintenance of recombination suppression on sex chromosomes. Significance StatementSex chromosomes have evolved countless times across eukaryotes and often lose the ability to recombine, causing them to degenerate over time. Why then, does recombination not restart to purge harmful mutations? By generating a high-quality genome assembly of the blackspotted stickleback, we discovered the strong empirical evidence of a sex chromosome undergoing a double-crossover event within a "non-recombining" region, which reset the degenerative process. This finding challenges the view that sex chromosome decay is a one-way street. Furthermore, using forward evolutionary simulations, we demonstrate that the genetic signatures left by such events could help identify the selective forces acting within non-recombining sex chromosomes, thereby explaining the maintenance of recombination suppression.

evolutionary biology↗

Pervasive Intraspecific Genetic Local Adaptation Within the Natural Gut Microbiome

Gut microbial communities are shaped by the physicochemical gradients and compartmentalization along the gastrointestinal tract. Whether spatially variable selection is strong enough to promote lasting genetic divergence within microbial species subject to migration and clonal expansion remains unclear. We performed a metagenomic population-genetic analysis of roe deer microbiota across metabolically and structurally distinct gut compartments. Remarkably, 10 of 20 prevalent bacterial species exhibited clear signatures of genetic local adaptation, despite the homogenizing effects of frequent migration. Nutrient availability and environmental stability emerged as primary drivers of selection, with horizontal gene transfer as a key mechanism enabling local adaptation. Our findings demonstrate that a comprehensive understanding of ecological and evolutionary dynamics in the gut necessitates considering fine-scale genetic variation within species.

evolutionary biology↗

Evolution of functional genomic diversity during a bottleneck

Most species have been through population bottlenecks and range expansions, and the impact of these events on patterns of diversity has been well studied. In particular, it has been shown that initially rare neutral variants could readily fix on the front of range expansions or during bottlenecks, giving genomic signatures looking like selective sweeps. Here we expand on previous work by considering the dynamics of genomic diversity in (functional) regions harbouring deleterious variants during bottlenecks or during range expansions modelled as serial founder effects. We find that regions with very low levels of diversity (troughs) looking like selective sweeps can also readily form in these functional regions. Additionally, their properties depend on the dominance level of deleterious mutations. Trough density is higher and increases more rapidly in regions with co-dominant deleterious mutations than in regions with recessive mutations. Interestingly, we find that genetic diversity declines less rapidly in regions with partially recessive mutations than in regions with codominant ones or in regions with only neutral mutations. These features are generally enhanced in low recombination regions and for intermediate selection coefficients. If most deleterious mutations in a genome are partially recessive, it follows that functional low recombination regions should better preserve genetic diversity during range expansions than neutral regions of the genome. Significance statementMost research on the effects of selection on genetic diversity have been done in equilibrium populations, leaving a gap in our understanding of how selection acting on functional regions interacts with demographic changes. Our study reveals strikingly different impacts of purifying selection on genetic diversity depending on the dominance coefficient of deleterious mutations. While codominant variants create diversity dips resembling selective sweeps, recessive mutations can preserve genetic diversity during bottlenecks through the relatively understudied phenomenon of pseudo-overdominance. Our findings show how selective and demographic forces interact in more complex ways than previously thought and emphasize the importance of further exploring these dynamics to accurately interpret genetic variation in natural populations.

genetics↗

A generalized structured coalescent for purifying selection without recombination

Purifying selection is a critical factor in shaping genetic diversity. Current theoretical models only address scenarios of either very weak or strong selection, leaving a significant gap in our knowledge. The effects of purifying selection on patterns of genomic diversity remain poorly understood when selection against deleterious mutations is weak to moderate, particularly when recombination is limited or absent. In this study, we extend an existing approach, the fitness-class coalescent, to incorporate arbitrary levels of purifying selection. This model offers a comprehensive framework for exploring the influence of purifying selection in a wide range of demographic scenarios. Moreover, our research reveals potential sources of qualitative and quantitative biases in demographic inference, highlighting the significant risk of attributing genetic patterns to past demographic events rather than purifying selection. This work expands our understanding of the complex interplay between selection, drift, and population dynamics, and how purifying selection distorts demographic inference.

genetics↗

Scoary2: Rapid association of phenotypic multi-omics data with microbial pan-genomes

Genomic screening of bacteria is common practice to select strains with desired properties. However, 40-60% of all bacterial genes are still unknown, making capturing the phenotype an important part of the selection process. While omics-technologies collect high-dimensional phenotypic data, it remains challenging to link this information to genomic data to elucidate the impact of specific genes on phenotype. To this end, we present Scoary2, an ultra-fast software for microbial genome-wide association studies (mGWAS), enabling integrative data exploration. As proof of concept, we explore the metabolome of 44 yogurts with different strains of Propionibacterium freudenreichii, discovering two genes affecting carnitine metabolism.

bioinformatics↗

Strong neutral sweeps occurring during a population contraction

A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to similar reduction in local diversity, especially when the population experiences changes in population size, e.g., bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such "neutral sweeps" and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. We apply our framework to the case of a putative selective sweep signal around the gene Quetzalcoatl in D. melanogaster and show that the valley of diversity in the vicinity of this gene is compatible with a short bottleneck scenario without selection. Our findings provide further insight in how simple demographic models can create valleys of genetic diversity that may falsely be attributed to positive selection.

evolutionary biology↗

Gene surfing of underdominant alleles promotes formation of hybrid zones

The distribution of genetic diversity over geographic space has long been investigated in population genetics and serves as a useful tool to understand evolution and history of populations. Within some species or across regions of contact between two species, there are instances where there is no apparent ecological determinant of sharp changes in allele frequencies or divergence. To further understand these patterns of spatial genetic structure and potential species divergence, we model the establishment of clines that occur due to the surfing of underdominant alleles during range expansions. We provide analytical approximations for the fixation probability of underdominant alleles at expansion fronts and demonstrate that gene surfing can lead to clines in 1D range expansions. We extend these results to multiple loci via a mixture of analytical theory and individual-based simulations. We study the interaction between the strength of selection against heterozygotes, migration rates, and local recombination rates on the formation of stable hybrid zones. A key result of our study is that clines created by surfing at different loci can attract each other and align after expansion, if they are sufficiently close in space and in terms of recombination distance. Our findings suggest that range expansions can set the stage for parapatric speciation due to the alignment of multiple selective clines, even in the absence of ecologically divergent selection.

evolutionary biology↗

Genetic load may increase or decrease with selfing depending upon the recombination environment

The ability of natural selection to remove deleterious mutations from a population is a function of the effective population size. Increases in selfing rate, and concomitant increases in population-level homozygosity, can increase or decrease the efficacy of selection, depending on the dominance and selection coefficients of the deleterious mutations. Most theory has focused on how (partial) selfing affects the efficacy of selection for mutations of a given dominance and fitness effect in isolation. It remains unclear how selfing affects the purging of deleterious mutations in a genome-wide context where mutations with different selection and dominance coefficients co-segregate. Here, we use computer simulations to investigate how mutation, selection and recombination interact with selfing rate to shape genome-wide patterns of genetic load. We recover various mechanisms previously described for how (partial) selfing affects the efficacy of selection against mutations of a given dominance class. However, we find that the interaction of purifying selection against mutations of different dominance classes changes with selfing rate. In particular, as outcrossing populations transition from purifying selection to pseudo-overdominance they experience a dramatic increase in the genetic load caused by additive, mildly deleterious mutations. We describe the threshold selfing rate that prevents pseudo-overdominance and decreases genetic load.

genetics↗

Fragmentation helps evolutionary rescue in highly connected habitats

Genetic variation and population sizes are critical factors for successful adaptation to novel environmental conditions. Gene flow between sub-populations is a potent mechanism to provide such variation and can hence facilitate adaptation, for instance by increasing genetic variation or via the introduction of beneficial variants. On the other hand, if gene flow between different habitats is too strong, locally beneficial alleles may not be able to establish permanently. In the context of evolutionary rescue, intermediate levels of gene flow are therefore often optimal for maximizing a species chance for survival in metapopulations without spatial structure. To which extent and under which conditions gene flow facilitates or hinders evolutionary rescue in spatially structured populations remains unresolved. We address this question by studying the differences between evolutionary rescue in the island model and in the stepping stone model in a gradually deteriorating habitat. We show that evolutionary rescue is modulated by the rate of gene flow between different habitats, which in turn depends strongly on the spatial structure and the pattern of environmental deterioration. We use these insights to show that in many cases spatially structured models can be translated into a simpler island model using an appropriately scaled effective migration rate.

molecular biology↗

Transition from background selection to associative overdominance promotes diversity in regions of low recombination

Linked selection is a major driver of genetic diversity. Selection against deleterious mutations removes linked neutral diversity (background selection, BGS, Charlesworth et al. 1993), creating a positive correlation between recombination rates and genetic diversity. Purifying selection against recessive variants, however, can also lead to associative overdominance (AOD, Ohta 1971, Zhao & Charlesworth, 2016), due to an apparent heterozygote advantage at linked neutral loci that opposes the loss of neutral diversity by BGS. Zhao & Charlesworth (2016) identified the conditions when AOD should dominate over BGS in a single-locus model and suggested that the effect of AOD could become stronger if multiple linked deleterious variants co-segregate. We present a model describing how and under which conditions multi-locus dynamics can amplify the effects of AOD. We derive the conditions for a transition from BGS to AOD due to pseudo-overdominance (Ohta & Kimura 1970), i.e. a form of balancing selection that maintains complementary deleterious haplotypes that mask the effect of recessive deleterious mutations. Simulations confirm these findings and show that multi-locus AOD can increase diversity in low recombination regions much more strongly than previously appreciated. While BGS is known to drive genome-wide diversity in humans (Pouyet et al. 2018), the observation of a resurgence of genetic diversity in regions of very low recombination is indicative of AOD. We identify 21 such regions in the human genome showing clear signals of multi-locus AOD. Our results demonstrate that AOD may play an important role in the evolution of low recombination regions of many species.

evolutionary biology↗

When does gene flow facilitate evolutionary rescue?

AO_SCPLOWBSTRACTC_SCPLOWExperimental and theoretical studies have highlighted the impact of gene flow on the probability of evolutionary rescue in structured habitats. Mathematical modelling and simulations of evolutionary rescue in spatially or otherwise structured populations showed that intermediate migration rates can often maximize the probability of rescue in gradually or abruptly deteriorating habitats. These theoretical results corroborate the positive effect of gene flow on evolutionary rescue that has been identified in experimental yeast populations. The observations that gene flow can facilitate adaptation are in seeming conflict with traditional population genetics results that show that gene flow usually hampers (local) adaptation. Identifying conditions for when gene flow facilitates survival chances of populations rather than reducing them remains a key unresolved theoretical question. We here present a simple analytically tractable model for evolutionary rescue in a two-deme model with gene flow. Our main result is a simple condition for when migration facilitates evolutionary rescue, as opposed as no migration. We further investigate the roles of asymmetries in gene flow and / or carrying capacities, and the effects of density regulation and local growth rates on evolutionary rescue.

evolutionary biology↗

Evolution of dispersal can rescue populations from expansion load

Understanding the causes and consequences of range expansions or range shifts has a long history in evolutionary biology. Recent theoretical, experimental, and empirical work has identified two particularly interesting phenomena in the context of species range expansions: (i) gene surfing and the relaxation of natural selection, and (ii) spatial sorting. The former can lead to an accumulation of deleterious mutations at range edges, causing an expansion load and slowing down expansion. The latter can create gradients in dispersal-related traits along the expansion axis and cause an acceleration of expansion. We present a theoretical framework that treats spatial sorting and gene surfing as spatial versions of natural selection and genetic drift, respectively. This model allows us to study analytically how gene surfing and spatial sorting interact, and to derive the probability of fixation of pleiotropic mutations at the expansion front. We use our results to predict the co-evolution of mean fitness and dispersal rates, taking into account the effects of random genetic drift, natural selection and spatial sorting, as well as correlations between fitnessand dispersal-related traits. We identify a \"rescue effect\" of spatial sorting, where the evolution of higher dispersal rates at the leading edge rescues the population from incurring expansion load.

evolutionary biology↗

Genomic analysis of fast expanding bacteria reveals new molecular adaptive mechanisms

Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative effects of range expansions. We investigated the molecular evolution of 20 lines (SEL) selected for fast expansions and compared them to 20 lines without artificial selection (CONTROL). We find that all 20 SEL lines have been able to increase their expansion speed relative to the ancestral line, unlike CONTROL lines, showing that enough beneficial mutations are produced during spatial expansions to counteract the negative effect of expansion load. Importantly, SEL and CONTROL lines have similar numbers of mutations indicating that they evolved for the same number of generations and that increased fitness is not due to a purging of deleterious mutations. We find that loss of function (LOF) mutations are better at explaining the increased expansion speed of SEL lines than non-synonymous mutations or a combination of the two. Interestingly, most LOF mutations are found in simple sequence repeats located in genes involved in gene regulation and gene expression. We postulate that such potentially reversible mutations could play a major role in the rapid adaptation of bacteria to changing environmental conditions by shutting down expensive genes and adjusting gene expression.\n\nAuthor SummaryWe investigated if strong artificial selection for fast expansion can counteract the negative effects of range expansion which had been shown to lead to an accumulation of deleterious mutations. This experiments showed that i) an increase in expansion speed could occur if bacteria were selected from the largest protruding sectors, and ii) that artificially selected bacterial lines accumulated about the same number of mutations than simply expanding line suggesting that the observed increased fitness is not due to increased purifying selection where deleterious mutations would have been removed in fast growing lines. We find that loss of function (LOF) mutations are best explaining the observed increased expansion speed in selected lines. These mutations, which are known to play an important role in adaptive processes in bacterial populations, frequently consist in small insertion-deletions in simple sequence repeats, and are thus relatively easily reversible. They could thus act as switches that can reversibly shut down genes. Our results therefore suggest that shutting down expensive genes and adjusting gene expression are important for adaptive processes during range expansion.

evolutionary biology↗

Mutation load dynamics during environmentally-driven range shifts

The fitness of spatially expanding species has been shown to decrease over time and space, but specialist species tracking their changing environment and shifting their range accordingly have been little studied. We use individual-based simulations and analytical modeling to compare the impact of range expansions and range shifts on genetic diversity and fitness loss, as well as the ability to recover fitness after either a shift or expansion. We find that the speed of a shift has a strong impact on fitness evolution. Fastest shifts show the strongest fitness loss per generation, but intermediate shift speeds lead to the strongest fitness loss per geographic distance. Range shifting species lose fitness more slowly through time than expanding species, however, their fitness compared at equivalent geographic distances spread can be considerably lower. These counter-intuitive results arise from the combination of time over which selection acts and mutations enter the system. Range shifts also exhibit reduced fitness recovery after a geographic shift and may result in extinction, whereas range expansions can persist from the core of the species range. The complexity of range expansions and range shifts highlights the potential for severe consequences of environmental change on species survival.\n\nAuthor SummaryAs environments change through time across the globe, species must adapt or relocate to survive. Specialized species must track the specific moving environments to which they are adapted, as compared to generalists which can spread widely. During colonization of new habitat, individuals can accumulate deleterious alleles through repeated bottlenecks. We show through simulation and analytic modeling that the process by which these alleles accumulate changes depending upon the speed at which populations spread over a landscape. This is due to the increased efficacy of selection against deleterious variants at slow speeds of range shifts and decreased input of mutations at faster speeds of range shifts. Under some selective circumstances, shifting of a species range leads to extinction of the entire population. This suggests that the rate of environmental change across the globe will play a large role in the survival of specialist species as compared to more generalist species.

evolutionary biology↗

Establishment of locally adapted mutations under divergent selection

We study the establishment probabilities of locally adapted mutations using a multitype branching process framework. We find a surprisingly simple and intuitive analytical approximation for the establishment probabilities in a symmetric two-deme model under the assumption of weak (positive) selection. This is the first analytical closed-form approximation for arbitrary migration rate to appear in the literature. We find that the establishment probability lies between the weak and the strong migration limits if we condition the origin of the mutation to the deme where it is advantageous. This is not the case when we condition the mutation to first occur in a deme where it is disadvantageous. In this case we find that an intermediate migration rate maximizes the probability of establishment. We extend our results to the cases of multiple demes, two demes with asymmetric rates of gene flow, and asymmetric carrying capacities. The latter case allows us to illustrate how density regulation can affect establishment probabilities. Finally we use our results to investigate the role of gene flow on the rate of local adaptation and identify cases in which intermediate amounts of gene flow facilitate the rate of local adaptation as compared to two populations without gene flow.

evolutionary biology↗