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Schlötterer, C.

Publications and source records attributed to Schlötterer, C..

9 recordsLinked to original sources
bioRxiv2025

Tracking polygenic adaptation: phenotypic stasis after rapid adaptation in large populations of Drosophila

Most adaptive traits have a polygenic basis, and their evolution in response to environmental change results from the cumulative effect of many underlying loci. Theoretical studies predict two phases of phenotypic evolution: an initial directional phase, characterized by shifts in the mean of the trait towards a new optimum; and a subsequent stabilizing phase, in which the mean phenotype remains constant. However, there is limited empirical evidence to confirm these predictions. We exposed six replicate populations of Drosophila simulans, each with 100,000 individuals, to a new high-protein diet for 31 generations. Using time-series of high-order and molecular phenotypes, we characterized the phases of polygenic adaptation and inferred the transition between the directional and stabilizing selection phases empirically. The initial (directional) phase was characterized by a rapid phenotypic response, followed by a plateau after seven generations of adaptation, suggesting proximity to the new trait optimum (i.e. the stabilizing phase). The phenotypic responses were highly parallel among the replicate populations throughout the experiment. The contribution of pleiotropic loci to adaptive phenotypic evolution varied across the different phases of adaptation. Adaptation throughout the experiment was mainly facilitated by genes with low-to-intermediate pleiotropy, while highly pleiotropic genes played a significant role in the initial phase of adaptation. Parallel evolutionary responses across the replicate populations were also driven by genes with low-to-intermediate pleiotropy. Our findings support the predictions of theoretical models and provide empirical evidence for directional and stabilizing phases of polygenic adaptation.

evolutionary biology↗
bioRxiv2024

Purifying Selection Shapes the Dynamics of P-element Invasion in Drosophila Populations

BackgroundTransposable elements (TEs) are DNA sequences that can move within a host genome. Many new TE insertions have deleterious effects on their host and are therefore removed by purifying selection. The genomic distribution of TEs thus reflects a balance between new insertions and purifying selection. However, the inference of purifying selection against deleterious TE insertions from the patterns observed in natural populations is challenged by the confounding effects of demographic events, such as population bottlenecks and migration. ResultsWe used Experimental Evolution to study the role of purifying selection during the invasion of the P-element, a highly invasive TE, in replicated Drosophila simulans populations under controlled laboratory conditions. Because the change in P-element copy number over time provides information about the transposition rate and the effect of purifying selection, we repeatedly sequenced the experimental populations to study the P-element invasion dynamics. Based on the empirical data, we used Gaussian Process surrogate models to efficiently explore the parameter space and identify parameter combinations that best reproduce the experimental P-element invasion trajectories. Assuming that beneficial P-element insertions are negligible, we found that, in our experimental populations, 73% (60.9% - 76.1%) of new P-element insertions are under purifying selection with a mean selection coefficient of -0.056 (-0.060 - -0.042), highlighting the central role of selection in shaping P-element invasion dynamics. ConclusionThis study underscores the power of Experimental Evolution as a tool for studying transposable element invasions and highlights the pivotal role of purifying selection in regulating P-element dynamics.

evolutionary biology↗
bioRxiv2024

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource

Large scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009-2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species demographic history and identify novel signs of adaptation across spatial and temporal dimensions. We showed that patterns of secondary contact, originally characterized in North America, are replicated in South America and Australia. We also found that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatio-temporal patterns of genetic variation in this classic model system.

evolutionary biology↗
bioRxiv2021

Pre- and post-mating reproductive isolation evolve independently during rapid adaptation to high temperature

BackgroundEcological speciation and mutation-order speciation are two different mechanisms of adaptation-driven speciation. Both mechanisms predict different patterns of reproductive isolation for replicate populations adapting to the same environment. With ecological speciation, barriers to gene flow emerge between populations from different environments, but not among replicate populations from the same environment. Mutation-order speciation predicts reproductive isolation among populations adapted to the same environment. ResultsWe demonstrate that both speciation processes occurred within about 100 generations when replicate Drosophila simulans populations adapted to a novel, hot environment. Gene expression analysis identified the underlying molecular mechanisms. Premating ecological speciation is the byproduct of an altered lipid metabolism, which also changed the cuticular hydrocarbon (CHC) composition in hot-evolved flies. Postmating reproductive isolation supports mutation-order speciation most likely driven by co-evolution of reproduction-associated genes. ConclusionAdaptation processes can rapidly induce incipient speciation and different speciation mechanisms affect pre- and postmating reproductive isolation. We propose that the definition of mutation-order speciation should be expanded to account for polygenic processes from standing genetic variation.

evolutionary biology↗
bioRxiv2021

Fine mapping without phenotyping: Identification of selection targets in secondary Evolve and Resequence experiments

Evolve and Resequence (E&R) studies investigate the genomic selection response of populations in an Experimental Evolution setup. Despite the popularity of E&R, empirical studies in sexually reproducing organisms typically suffer from an excess of candidate loci due to linkage disequilibrium, and single gene or SNP resolution is the exception rather than the rule. Recently, so-called "secondary E&R" has been suggested as promising experimental follow-up procedure to confirm putatively selected regions from a primary E&R study. Secondary E&R provides also the opportunity to increase mapping resolution by allowing for additional recombination events, which separate the selection target from neutral hitchhikers. Here, we use computer simulations to assess the effect of different crossing schemes, population size, experimental duration, and number of replicates on the power and resolution of secondary E&R. We find that the crossing scheme and population size are crucial factors determining power and resolution of secondary E&R: a simple crossing scheme with few founder lines consistently outcompetes crossing schemes where evolved populations from a primary E&R experiment are mixed with a complex ancestral founder population. Regardless of the experimental design tested, a population size of at least 4,800 individuals, which is roughly 5 times larger than population sizes in typical E&R studies, is required to achieve a power of at least 75%. Our study provides an important step towards improved experimental designs aiming to characterize causative SNPs in Experimental Evolution studies. SignificanceDespite the popularity of Evolve and Resequence (E&R) to investigate genomic selection responses, most studies that use sexually reproducing organisms have broad selection signatures and an excess of candidate loci due to linkage disequilibrium. In this study, we use computer simulations and statistical modelling to evaluate the effects of different experimental and population genetic parameters on the success of potential follow-up experiments (=secondary E&R) aiming to validate and fine-map selection signatures of primary studies. We found that a large population size in combination with a simple crossing scheme is key to the success of secondary E&R in Drosophila.

evolutionary biology↗
bioRxiv2020

The adaptive architecture is shaped by population ancestry and not by selection regime

Understanding the genetic architecture of adaptive phenotypes is a key question in evolutionary biology. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. The recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of loci under strong selection (19 selected alleles, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations have a pronounced impact on our understanding of adaptation in natural populations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

evolutionary biology↗
bioRxiv2020

Reversed sex-biased mutation rates for indels and base substitutions in Drosophila melanogaster

Sex biases in mutation rates may affect the rate of adaptive evolution. In many species, males have higher mutation rates than females when single nucleotide variants (SNVs) are considered. In contrast, indel mutations in humans and chimpanzees are female-biased. In Drosophila melanogaster, direct estimates of mutation rates did not uncover sex differences, but a recent analysis suggested the presence of male-biased SNVs mutations. Here we study the sex-specific mutation processes using mutation accumulation data from mismatch-repair deficient D. melanogaster. We find that sex differences in flies are similar to the ones observed in humans: a higher mutation rate for SNVs in males and a higher indel rate in females. These results have major implications for the study of neutral variation and adaptation in Drosophila.

evolutionary biology↗
bioRxiv2020

Transcription-coupled repair in Drosophila melanogaster is independent of the mismatch repair pathway

Transcription-coupled repair (TCR) removes base damage on the transcribed strand of a gene to ensure a quick resumption of transcription. Based on the absence of key enzymes for TCR and empirical evidence, TCR was thought to be missing in Drosophila melanogaster. The recent demonstration of TCR in S2 cells raises the question about the involved genes. Since the mismatch repair (MMR) pathway serves a central role in TCR, at least in Escherichia coli, we studied the mutational signatures in flies with a deletion of the MMR gene spellchecker1 (spel1), a MutS homolog. Whole-genome sequencing of mutation accumulation (MA) lines obtained 7,345 new single nucleotide variants (SNVs) and 5,672 short indel mutations, the largest data set from an MA study in D. melanogaster. Based on the observed mutational strand-asymmetries, we conclude that TCR is still active without spel1. The operation of TCR is further confirmed by a negative association between mutation rate and gene expression. Surprisingly, the TCR signatures are detected for introns, but not for exons. We propose that an additional exon-specific repair pathway is masking the signature of TCR. This study presents the first step towards understanding the molecular basis of TCR in Drosophila melanogaster.

molecular biology↗
bioRxiv2019

Low concordance of short-term and long-term selection responses in experimental Drosophila populations

AO_SCPLOWBSTRACTC_SCPLOWExperimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10 % of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.

molecular biology↗