Population bottlenecks can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, each founder that survives a bottleneck can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread more quickly. A theoretical model predicted that the rate of fitness gains should be maximized using ~8-fold dilutions. Here we investigate the impact of repeated bottlenecks on the dynamics of adaptation using numerical simulations and experimental populations of
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Escherichia coli . Our simulations confirm the model’s prediction when populations evolve in a regime where beneficial mutations are rare and waiting times between successful mutations are long. However, more extreme dilutions maximize fitness gains in simulations when beneficial mutations are common and clonal interference prevents most of them from fixing. To examine these predictions, we propagated 48E. coli populations with 2-, 8-, 100-, and 1000-fold dilutions for 150 days. Adaptation began earlier and fitness gains were greater with 100- and 1000-fold dilutions than with 8-fold dilutions, consistent with the simulations when beneficial mutations are common. However, the selection pressures in the 2-fold treatment were qualitatively different from the other treatments, violating a critical assumption of the model and simulations. Thus, varying the dilution factor during periodic bottlenecks can have multiple effects on the dynamics of adaptation caused by differential losses of diversity, different numbers of generations, and altered selection.Free, publicly-accessible full text available September 18, 2025 -
Rodríguez-Pastor, Ruth ; Hasik, Adam_Z ; Knossow, Nadav ; Bar-Shira, Enav ; Shahar, Naama ; Gutiérrez, Ricardo ; Zaman, Luis ; Harrus, Shimon ; Lenski, Richard_E ; Barrick, Jeffrey_E ; et al ( , Parasites & Vectors)
Abstract Background Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of
Bartonella and rodents from Israel’s northwestern Negev Desert. We chose to study this system because, in this region, 75–100% of rodents are infected withBartonella at any given time, despite an efficient immunological response. In this region,Bartonella species circulate in three rodent species, and we tested the hypothesis that at least one of these hosts exhibits a waning immune response toBartonella , which allows reinfections.Methods We inoculated captive animals of all three rodent species with the same
Bartonella strain, and we quantified the bacterial dynamics andBartonella -specific immunoglobulin G antibody kinetics over a period of 139 days after the primary inoculation, and then for 60 days following reinoculation with the same strain.Results Contrary to our hypothesis, we found a strong, long-lasting immunoglobulin G antibody response, with protective immunological memory in all three rodent species. That response prevented reinfection upon exposure of the rodents to the same
Bartonella strain.Conclusions This study constitutes an initial step toward understanding how the interplay between traits of
Bartonella and their hosts influences the epidemiological dynamics of these pathogens in nature.Graphical Abstract