Biology subjects

Limdi, A.

Publications and source records attributed to Limdi, A..

4 recordsLinked to original sources

bioRxiv2025

Sex decreases the pleiotropic costs of local adaptation

Understanding the evolutionary mechanisms that maintain sex throughout nature despite its substantial direct costs is a longstanding challenge in biology. Previous work has shown that sexual recombination provides a key advantage in speeding adaptation, in part by separating beneficial mutations from deleterious hitchhikers. However, these earlier studies have focused on the effects of sex in a constant environment. Here, we show that recombination also provides a key advantage in fluctuating conditions, promoting the evolution of generalist phenotypes by reducing the pleiotropic costs of local adaptation. Using laboratory evolution in S. cerevisiae as a model system, we show that hitchhiking genetic load leads to pleiotropic costs and hence specialization in response to local adaptation in asexual but not in sexual lineages. This provides the first direct evidence that sex can be maintained over longer evolutionary timescales because it enables lineages to persist in the face of environmental change.

evolutionary biology↗

bioRxiv2022

Resolving deleterious and near-neutral effects requires different pooled fitness assay designs

Pooled sequencing-based fitness assays are a powerful and widely used approach to quantifying fitness of thousands of genetic variants in parallel. Despite the throughput of such assays, they are prone to biases in fitness estimates, and errors in measurements are typically larger for deleterious fitness effects, relative to neutral effects. In practice, designing pooled fitness assays involves tradeoffs between the number of timepoints, the sequencing depth, and other parameters to gain as much information as possible within a feasible experiment. Here, we combined theory, simulations, and reanalysis of an existing experimental dataset to explore how assay parameters impact measurements of near-neutral and deleterious fitness effects. We found that sequencing multiple timepoints at relatively modest depth improved estimates of near-neutral fitness effects, but systematically biased measurements of deleterious effects. We identified a theoretical lower bound for estimates from bulk fitness assays, and showed that increasing sequencing depth, and reducing number of timepoints improved resolution of deleterious fitness effects. Our results highlight a tradeoff between measurement of deleterious and near-neutral effect sizes for a fixed amount of data and suggest that fitness assay design should be tuned for fitness effects that are relevant to the specific biological question.

evolutionary biology↗

bioRxiv2022

Parallel changes in gene essentiality over 50,000 generations of evolution

As evolving populations accumulate mutations, the benefits and costs of subsequent mutations change. As fitness increases, the relative benefit of new mutations typically decreases. However, the question remains whether deleterious mutations tend to have larger or smaller costs as a population adapts; theory and experiments provide support for both conflicting hypotheses. To address this question, we compared the effects of insertion mutations in every gene in Escherichia coli between ancestral and 12 independently derived strains after 50,000 generations in a uniform environment. We found both increases and decreases in the fitness costs of mutations, leaving the overall distribution of effects largely unchanged. However, at the extreme, more genes became essential over evolution than vice versa. Both changes in fitness effects and essentiality evolved in parallel across the independent populations, and most changes were not explained by structural variation or altered gene expression. Thus, the macroscopic features of the local fitness landscape remained largely unchanged, even as access to particular evolutionary trajectories changed consistently during adaptation to the experimental environment. One Sentence SummaryLimdi et al. report parallel changes in the cost of mutations in replicate lineages of a decades-long E. coli evolution experiment.

evolutionary biology↗

bioRxiv2017

Asymmetric migration decreases stability but increases resilience in a heterogeneous metacommunity

Many natural communities are spatially distributed, forming a network of subcommunities linked by migration. Migration patterns are often asymmetric and heterogeneous, with important consequences on the ecology and evolution of the species. Here we investigated experimentally how asymmetric migration and heterogeneous structure affect a simple metacommunity of budding yeast, formed by one strain that produces a public good and a non-producer strain that benefits from it. We find that asymmetric migration increases the fraction of producers in all subpopulations of the metacommunity. Furthermore, asymmetric migration decreases the metacommunitys tolerance to challenging environments, but increases its resilience to transient perturbations. This apparent paradox occurs because tolerance to a constant challenge depends on the weakest subpopulations of the network, while resilience to a transient perturbation depends on the strongest ones.\n\nOne Sentence SummaryAsymmetric migration decreases the stability of experimental yeast metacommunities but increases their resilience to transient shocks.

ecology↗