Biology subjects

Barghi, N.

Publications and source records attributed to Barghi, N..

5 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↗

bioRxiv2019

Distance to trait optimum is a crucial factor determining the genomic signature of polygenic adaptation

Polygenic adaptation is frequently associated with small allele frequency changes of many loci. Recent works suggest, that large allele frequency changes can be also expected. Laboratory natural selection (LNS) experiments provide an excellent experimental framework to study the adaptive architecture under controlled laboratory conditions: time series data in replicate populations evolving independently to the same trait optimum can be used to identify selected loci. Nevertheless, the choice of the new trait optimum in the laboratory is typically an ad hoc decision without consideration of the distance of the starting population to the new optimum. Here, we used forward-simulations to study the selection signatures of polygenic adaptation in populations evolving to different trait optima. Mimicking LNS experiments we analyzed allele frequencies of the selected alleles and population fitness at multiple time points. We demonstrate that the inferred adaptive architecture strongly depends on the choice of the new trait optimum in the laboratory and the significance cut-off used for identification of selected loci. Our results not only have a major impact on the design of future Evolve and Resequence (E&R) studies, but also on the interpretation of current E&R data sets.

evolutionary biology↗

bioRxiv2019

Distinct patterns of selective sweep and polygenic adaptation

The central paradigm of molecular population genetics is selective sweeps, where targets of selection have independent effects on the phenotype and quickly rise to fixation. In quantitative genetics, many loci contribute epistatically to adaptation and subtle frequency changes occur at many loci. Since both paradigms could result in a sweep-like genomic signature, additional criteria are needed to distinguish them. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles under both paradigms. We identify several distinct patterns of selective sweeps and polygenic adaptation in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two paradigms.\n\nAuthors summaryThe selective sweep model assumes an independent frequency increase of favorable alleles and has been the basis of many tests for selection. While, polygenic adaptation is typically modelled by small frequency shifts in many loci. Recently, some theoretical and empirical work demonstrated that polygenic adaptation, similar to sweep, could also results in pronounced allele frequency changes. These results suggest that other distinct features need to be identified. Using computer simulations, we identified distinctive features for each paradigm that can be used to differentiate the sweep model from polygenic adaptation. Features such as allele frequency trajectories, time-series fitness, distribution of selected alleles on haplotypes, and parallelism among replicates can be used for development of suitable tests to distinguish between different adaptive architectures. These features provide the basis for theoretical modeling, design of selection experiments and data analysis.

evolutionary biology↗

bioRxiv2019

Neuronal function and dopamine signaling evolve at high temperature in Drosophila

Introduction Introduction Main Methods Author contributions Competing interest Materials and Correspondence References Adaptation to local environments is a general principle in nature. In the light of the ongoing climatic change, the mechanisms for temperature adaptation are of particular interest1-2. Many essential biological processes are temperature sensitive, and neuronal activity3-7 is a particularly prominent one as it affects essential, fitness-related traits such as behavior and locomotion8. Here, we investigate if temperature stress triggers adaptation of neuronal signaling. We used replicated laboratory evolution experiments with Drosophila simula ...

evolutionary biology↗

bioRxiv2018

Polygenic adaptation fuels genetic redundancy in Drosophila

The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic - i.e. result from selection on a large number of genetic loci - but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; mean s=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

evolutionary biology↗