Daily Transfers, Archiving Populations, and Measuring Fitness in the Long-Term Evolution Experiment with Escherichia coli.

The Long-Term Evolution Experiment (LTEE) has followed twelve populations of Escherichia coli as they have adapted to a simple laboratory environment for more than 35 years and 77,000 bacterial generations. The setup and procedures used in the LTEE epitomize reliable and reproducible methods for studying microbial evolution. In this protocol, we first describe how the LTEE populations are transferred to fresh medium and cultured each day. Then, we describe how the LTEE populations are regularly checked for possible signs of contamination and archived to provide a permanent frozen "fossil record" for later study. Multiple safeguards included in these procedures are designed to prevent contamination, detect various problems when they occur, and recover from disruptions without appreciably setting back the progress of the experiment. One way that the overall tempo and character of evolutionary changes are monitored in the LTEE is by measuring the competitive fitness of populations and strains from the experiment. We describe how co-culture competition assays are conducted and provide both a spreadsheet and an R package (fitnessR) for calculating relative fitness from the results. Over the course of the LTEE, the behaviors of some populations have changed in interesting ways, and new technologies like whole-genome sequencing have provided additional avenues for investigating how the populations have evolved. We end by discussing how the original LTEE procedures have been updated to accommodate or take advantage of these changes. This protocol will be useful for researchers who use the LTEE as a model system for studying connections between evolution and genetics, molecular biology, systems biology, and ecology. More broadly, the LTEE provides a tried-and-true template for those who are beginning their own evolution experiments with new microbes, environments, and questions.

Patient Activation, Depressive Symptoms, and Self-Rated Health: Care Management Intervention Effects among High-Need, Medically Complex Adults.

The purpose of this randomized controlled trial (n = 268) at a Federally Qualified Health Center was to evaluate the outcomes of a care management intervention versus an attention control telephone intervention on changes in patient activation, depressive symptoms and self-rated health among a population of high-need, medically complex adults. Both groups had similar, statistically significant improvements in patient activation and self-rated health. Both groups had significant reductions in depressive symptoms over time; however, the group who received the care management intervention had greater reductions in depressive symptoms. Participants in both study groups who had more depressive symptoms had lower activation at baseline and throughout the 12 month study. Findings suggest that patients in the high-need, medically complex population can realize improvements in patient activation, depressive symptoms, and health status perceptions even with a brief telephone intervention. The importance of treating depressive symptoms in patients with complex health conditions is highlighted.

The MODES Toolbox: Measurements of Open-Ended Dynamics in Evolving Systems.

Building more open-ended evolutionary systems can simultaneously advance our understanding of biology, artificial life, and evolutionary computation. In order to do so, however, we need a way to determine when we are moving closer to this goal. We propose a set of metrics that allow us to measure a system's ability to produce commonly-agreed-upon hallmarks of open-ended evolution: change potential, novelty potential, complexity potential, and ecological potential. Our goal is to make these metrics easy to incorporate into a system, and comparable across systems so that we can make coherent progress as a field. To this end, we provide detailed algorithms (including C++ implementations) for these metrics that should be easy to incorporate into existing artificial life systems. Furthermore, we expect this toolbox to continue to grow as researchers implement these metrics in new languages and as the community reaches consensus about additional hallmarks of open-ended evolution. For example, we would welcome a measurement of a system's potential to produce major transitions in individuality. To confirm that our metrics accurately measure the hallmarks we are interested in, we test them on two very different experimental systems: NK landscapes and the Avida digital evolution platform. We find that our observed results are consistent with our prior knowledge about these systems, suggesting that our proposed metrics are effective and should generalize to other systems.

Fluctuating environments select for short-term phenotypic variation leading to long-term exploration.

Genetic spaces are often described in terms of fitness landscapes or genotype-to-phenotype maps, where each genetic sequence is associated with phenotypic properties and linked to other genotypes that are a single mutational step away. The positions close to a genotype make up its "mutational landscape" and, in aggregate, determine the short-term evolutionary potential of a population. Populations with wider ranges of phenotypes in their mutational neighborhood are known to be more evolvable. Likewise, those with fewer phenotypic changes available in their local neighborhoods are more mutationally robust. Here, we examine whether forces that change the distribution of phenotypes available by mutation profoundly alter subsequent evolutionary dynamics. We compare evolved populations of digital organisms that were subject to either static or cyclically-changing environments. For each of these, we examine diversity of the phenotypes that are produced through mutations in order to characterize the local genotype-phenotype map. We demonstrate that environmental change can push populations toward more evolvable mutational landscapes where many alternate phenotypes are available, though purely deleterious mutations remain suppressed. Further, we show that populations in environments with harsh changes switch phenotypes more readily than those in environments with more benign changes. We trace this effect to repeated population bottlenecks in the harsh environments, which result in shorter coalescence times and keep populations in regions of the mutational landscape where the phenotypic shifts in question are more likely to occur. Typically, static environments select solely for immediate optimization, at the expensive of long-term evolvability. In contrast, we show that with changing environments, short-term pressures to deal with immediate challenges can align with long-term pressures to explore a more productive portion of the mutational landscape.

Open-Ended Evolution: Perspectives from the OEE Workshop in York.

We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshop's talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE-it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1 .

Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli.

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely--or at least for a long time--even in a constant environment.

A Comparison of Methods to Measure Fitness in Escherichia coli.

In order to characterize the dynamics of adaptation, it is important to be able to quantify how a population's mean fitness changes over time. Such measurements are especially important in experimental studies of evolution using microbes. The Long-Term Evolution Experiment (LTEE) with Escherichia coli provides one such system in which mean fitness has been measured by competing derived and ancestral populations. The traditional method used to measure fitness in the LTEE and many similar experiments, though, is subject to a potential limitation. As the relative fitness of the two competitors diverges, the measurement error increases because the less-fit population becomes increasingly small and cannot be enumerated as precisely. Here, we present and employ two alternatives to the traditional method. One is based on reducing the fitness differential between the competitors by using a common reference competitor from an intermediate generation that has intermediate fitness; the other alternative increases the initial population size of the less-fit, ancestral competitor. We performed a total of 480 competitions to compare the statistical properties of estimates obtained using these alternative methods with those obtained using the traditional method for samples taken over 50,000 generations from one of the LTEE populations. On balance, neither alternative method yielded measurements that were more precise than the traditional method.

Long-term dynamics of adaptation in asexual populations.

Experimental studies of evolution have increased greatly in number in recent years, stimulated by the growing power of genomic tools. However, organismal fitness remains the ultimate metric for interpreting these experiments, and the dynamics of fitness remain poorly understood over long time scales. Here, we examine fitness trajectories for 12 Escherichia coli populations during 50,000 generations. Mean fitness appears to increase without bound, consistent with a power law. We also derive this power-law relation theoretically by incorporating clonal interference and diminishing-returns epistasis into a dynamical model of changes in mean fitness over time.

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.

Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼150-fold, whereas the mutY mutations reduced the rate by ∼40-60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined.