Specific adaptation to strong competitors can offset the negative effects of population size reductions

Experimental evolution for cell biology

Evolutionary cell biology explores the origins, principles, and core functions of cellular features and regulatory networks through the lens of evolution. This emerging field relies heavily on comparative experiments and genomic analyses that focus exclusively on extant diversity and historical events, providing limited opportunities for experimental validation. In this opinion article, we explore the potential for experimental laboratory evolution to augment the evolutionary cell biology toolbox, drawing inspiration from recent studies that combine laboratory evolution with cell biological assays. Primarily focusing on approaches for single cells, we provide a generalizable template for adapting experimental evolution protocols to provide fresh insight into long-standing questions in cell biology.

Interspecific Niche Competition Increases Morphological Diversity in Multi-Species Microbial Communities

Intraspecific competition for limited niches has been recognized as a driving force for adaptive radiation, but results for the role of interspecific competition have been mixed. Here, we report the adaptive diversification of the model bacteria Pseudomonas fluorescens in the presence of different numbers and combinations of four competing bacterial species. Increasing the diversity of competitive community increased the morphological diversity of focal species, which is caused by impeding the domination of a single morphotype. Specifically, this pattern was driven by more diverse communities being more likely to contain key species that occupy the same niche as otherwise competitively superior morphotype, and thus preventing competitive exclusion within the focal species. Our results suggest that sympatric adaptive radiation is driven by the presence or absence of niche-specific competitors.

Performance in a novel environment subject to ghost competition

Background

A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary dynamics within the community.

Methods

Here we report the long-term influence of a ghost competitor on the performance of a more successful species using experimental evolution. We transferred the spider mite Tetranychus urticae onto a novel host plant under initial presence or absence of a competing species, the congeneric mite T. ludeni.

Results

The competitor species, T. ludeni, unintentionally went extinct soon after the start of the experiment, but we nevertheless completed the experiment and found that the early competitive pressure of this ghost competitor positively affected the performance (i.e., fecundity) of the surviving species, T. urticae. This effect on T. urticae lasted for at least 25 generations.

Discussion

Our study suggests that early experienced selection pressures can exert a persistent evolutionary signal on species’ performance in novel environments.

Specific adaptation to strong competitors can offset the negative effects of population size reductions

Competition plays a crucial role in determining adaptation of species, yet we know little as to how adaptation is affected by the strength of competition. On the one hand, strong competition typically results in population size reductions, which can hamper adaptation owing to a shortage of beneficial mutations; on the other hand, specificity of adaptation to competitors may offset the negative evolutionary consequences of such population size effects. Here, we investigate how competition strength affects population fitness in the bacterium Pseudomonas fluorescens Our results demonstrate that strong competition constrains adaptation of focal populations, which can be partially explained by population size reductions. However, fitness assays also reveal specific adaptation of focal populations to particular competitors varying in competitive ability. Additionally, this specific adaptation can offset the negative effects of competitor-mediated population size reductions under strong competition. Our study, therefore, highlights the importance of opposing effects of strong competition on species adaptation, which may lead to different outcomes of colonization under intense and relaxed competitive environments in the context of population dispersal.

Competitive species interactions constrain abiotic adaptation in a bacterial soil community

Studies of abiotic adaptation often consider single species in isolation, yet natural communities contain many coexisting species which could limit or promote abiotic adaptation. Here we show, using soil bacterial communities, that evolving in the presence of a competitor constrained abiotic adaptation. Specifically, Pseudomonas fluorescens evolved alone was fitter than P. fluorescens evolved alongside Pseudomonas putida, when P. putida was absent. Genome analyses indicated this was due to mutation of the acetate scavenger actP, which occurred exclusively, and almost universally, in single‐species‐evolved clones. actP disruption was associated with increased growth in soil compared with wild‐type actP, but this benefit was abolished when P. putida was present, suggesting a role for carbon scavenging transporters in species interactions, possibly through nutrient competition. Our results show that competitive species interactions can limit the evolutionary response to abiotic selection, because the fitness benefits of abiotic adaptive mutations were negated in more complex communities.

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.