Susan F. Bailey

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.

Experimental evolution (EE) combined with whole‐genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE‐WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively small genome sizes. These experiments are particularly suited to answer long‐standing questions such as: How many mutations underlie adaptive evolution, and how are they distributed across the genome and through time? Are there general rules or principles governing which genes contribute to adaptation, and are certain kinds of genes more likely to be targets than others? How common is epistasis among adaptive mutations, and what does this reveal about the variety of genetic routes to adaptation? How common is parallel evolution, where the same mutations evolve repeatedly and independently in response to similar selective pressures? Here, we summarize the significant findings of this body of work, identify important emerging trends and propose promising directions for future research. We also outline an example of a computational pipeline for use in EE‐WGS studies, based on freely available bioinformatics tools.

The effect of selection environment on the probability of parallel evolution

Across the great diversity of life, there are many compelling examples of parallel and convergent evolution-similar evolutionary changes arising in independently evolving populations. Parallel evolution is often taken to be strong evidence of adaptation occurring in populations that are highly constrained in their genetic variation. Theoretical models suggest a few potential factors driving the probability of parallel evolution, but experimental tests are needed. In this study, we quantify the degree of parallel evolution in 15 replicate populations of Pseudomonas fluorescens evolved in five different environments that varied in resource type and arrangement. We identified repeat changes across multiple levels of biological organization from phenotype, to gene, to nucleotide, and tested the impact of 1) selection environment, 2) the degree of adaptation, and 3) the degree of heterogeneity in the environment on the degree of parallel evolution at the gene-level. We saw, as expected, that parallel evolution occurred more often between populations evolved in the same environment; however, the extent of parallel evolution varied widely. The degree of adaptation did not significantly explain variation in the extent of parallelism in our system but number of available beneficial mutations correlated negatively with parallel evolution. In addition, degree of parallel evolution was significantly higher in populations evolved in a spatially structured, multiresource environment, suggesting that environmental heterogeneity may be an important factor constraining adaptation. Overall, our results stress the importance of environment in driving parallel evolutionary changes and point to a number of avenues for future work for understanding when evolution is predictable.

Competition both drives and impedes diversification in a model adaptive radiation

Competitors are known to be important in governing the outcome of evolutionary diversification during an adaptive radiation, but the precise mechanisms by which they exert their effects remain elusive. Using the model adaptive radiation of Pseudomonas fluorescens, we show experimentally that the effect of competition on diversification of a focal lineage depends on both the strength of competition and the ability of the competitors to diversify. We provide evidence that the extent of diversification in the absence of interspecific competitors depends on the strength of resource competition. We also show that the presence of competitors can actually increase diversity by increasing interspecific resource competition. Competitors that themselves are able to diversify prevent diversification of the focal lineage by removing otherwise available ecological opportunities. These results suggest that the progress of an adaptive radiation depends ultimately on the strength of resource competition, an effect that can be exaggerated or impeded by the presence of competitors.

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

Conventional wisdom holds that synonymous mutations, nucleotide changes that do not alter the encoded amino acid, have no detectable effect on phenotype or fitness. However, a growing body of evidence from both comparative and experimental studies suggests otherwise. Synonymous mutations have been shown to impact gene expression, protein folding and fitness, however, direct evidence that they can be positively selected, and so contribute to adaptation, is lacking. Here we report the recovery of two beneficial synonymous single base pair changes that arose spontaneously and independently in an experimentally evolved population of Pseudomonas fluorescens. We show experimentally that these mutations increase fitness by an amount comparable to non-synonymous mutations and that the fitness increases stem from increased gene expression. These results provide unequivocal evidence that synonymous mutations can drive adaptive evolution and suggest that this class of mutation may be underappreciated as a cause of adaptation and evolutionary dynamics.

Effects of new mutations on fitness: insights from models and data

The rates and properties of new mutations affecting fitness have implications for a number of outstanding questions in evolutionary biology. Obtaining estimates of mutation rates and effects has historically been challenging, and little theory has been available for predicting the distribution of fitness effects (DFE); however, there have been recent advances on both fronts. Extreme‐value theory predicts the DFE of beneficial mutations in well‐adapted populations, while phenotypic fitness landscape models make predictions for the DFE of all mutations as a function of the initial level of adaptation and the strength of stabilizing selection on traits underlying fitness. Direct experimental evidence confirms predictions on the DFE of beneficial mutations and favors distributions that are roughly exponential but bounded on the right. A growing number of studies infer the DFE using genomic patterns of polymorphism and divergence, recovering a wide range of DFE. Future work should be aimed at identifying factors driving the observed variation in the DFE. We emphasize the need for further theory explicitly incorporating the effects of partial pleiotropy and heterogeneity in the environment on the expected DFE.

Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature

There have been a variety of approaches taken to try to characterize and identify the genetic basis of adaptation in nature, spanning theoretical models, experimental evolution studies and direct tests of natural populations. Theoretical models can provide formalized and detailed hypotheses regarding evolutionary processes and patterns, from which experimental evolution studies can then provide important proofs of concepts and characterize what is biologically reasonable. Genetic and genomic data from natural populations then allow for the identification of the particular factors that have and continue to play an important role in shaping adaptive evolution in the natural world. Further to this, experimental evolution studies allow for tests of theories that may be difficult or impossible to test in natural populations for logistical and methodological reasons and can even generate new insights, suggesting further refinement of existing theories. However, as experimental evolution studies often take place in a very particular set of controlled conditions – that is simple environments, a small range of usually asexual species, relatively short timescales – the question remains as to how applicable these experimental results are to natural populations. In this review, we discuss important insights coming from experimental evolution, focusing on four key topics tied to the evolutionary genetics of adaptation, and within those topics, we discuss the extent to which the experimental work compliments and informs natural population studies. We finish by making suggestions for future work in particular a need for natural population genomic time series data, as well as the necessity for studies that combine both experimental evolution and natural population approaches.

Spatial Structure of Ecological Opportunity Drives Adaptation in a Bacterium

Abundant ecological opportunity is thought to drive adaptation and diversification. The presence of multiple opportunities leads to divergent selection, which can slow adaptation when niche-specific beneficial mutations have antagonistically pleiotropic effects. Alternately, competition for multiple opportunities can generate divergent selection, which leads to high rates of adaptive differentiation. Which outcome occurs may depend on the spatial structure of those ecological opportunities. In a mixture of resources, competition for multiple opportunities can drive divergent selection; however, if each resource is available in a spatially distinct patch, simultaneous competition for multiple opportunities cannot occur. We report the effects of the extent and spatial structure of ecological opportunity on the evolutionary dynamics of populations of Pseudomonas fluorescens over 1,000 generations. We varied the extent of ecological opportunity by varying the number of sugar resources (mannose, glucose, and xylose), and we varied spatial structure by providing resources in either mixtures or spatially distinct patches. We saw that a particularly novel resource (xylose) drove the rate of adaptation when provided in a mixture but had no effect on diversity. Instead, we saw the evolution of a single adaptive strategy that differed with respect to phenotype and degree of specialization, depending on both the extent and the spatial structure of ecological opportunity.

Evolution of Fitness Trade-Offs in Locally Adapted Populations of Pseudomonas fluorescens*

Local adaptation seems to be common in natural systems, but the genetic causes of its evolution remain poorly understood. Here we characterize the genetic causes of trade-offs generating local adaptation in populations of Pseudomonas fluorescens that had previously been evolved for specialization on three different carbon resources. We measured the fitness effects of mutations that arose during selection in that environment and in alternative environments to quantify the degree of specialization. We find that all mutations are beneficial in the environment of selection and that those arising later during adaptation are associated with increasingly antagonistic effects in alternative environments compared with those arising earlier, consistent with a multioptima version of Fisher’s geometric model of adaptation. We also find that fitness of pairs of beneficial mutations are consistently less than additive in selection environments, producing a pattern of diminishing returns, but are more variable in alternative environments, being either positive or negative. Finally, we find that mutations in genes associated with loss of motility are beneficial across all environments, whereas mutations involving other functions, such as gene regulation, had more variable effects, being more environment specific. Taken together, these results provide a detailed account of the genetics of specialization and suggest that the evolution of trade-offs associated with local adaptation may often result from the antagonistic effects of beneficial mutations substituted later in adaptation.

What drives parallel evolution

Parallel evolution is the repeated evolution of the same phenotype or genotype in evolutionarily independent populations. Here, we use evolve‐and‐resequence experiments with bacteria and yeast to dissect the drivers of parallel evolution at the gene level. A meta‐analysis shows that parallel evolution is often rare, but there is a positive relationship between population size and the probability of parallelism. We present a modeling approach to estimate the contributions of mutational and selective heterogeneity across a genome to parallel evolution. We show that, for two experiments, mutation contributes between ∼10 and 45%, respectively, of the variation associated with selection. Parallel evolution cannot, therefore, be interpreted as a phenomenon driven by selection alone; it must also incorporate information on heterogeneity in mutation rates along the genome. More broadly, the work discussed here helps lay the groundwork for a more sophisticated, empirically grounded theory of parallel evolution.

Fitness declines towards range limits and local adaptation to climate affect dispersal evolution during climate‐induced range shifts

Dispersal ability will largely determine whether species track their climatic niches during climate change, a process especially important for populations at contracting (low‐latitude/low‐elevation) range limits that otherwise risk extinction. We investigate whether dispersal evolution at contracting range limits is facilitated by two processes that potentially enable edge populations to experience and adjust to the effects of climate deterioration before they cause extinction: (i) climate‐induced fitness declines towards range limits and (ii) local adaptation to a shifting climate gradient. We simulate a species distributed continuously along a temperature gradient using a spatially explicit, individual‐based model. We compare range‐wide dispersal evolution during climate stability vs. directional climate change, with uniform fitness vs. fitness that declines towards range limits (RLs), and for a single climate genotype vs. multiple genotypes locally adapted to temperature. During climate stability, dispersal decreased towards RLs when fitness was uniform, but increased when fitness declined towards RLs, due to highly dispersive genotypes maintaining sink populations at RLs, increased kin selection in smaller populations, and an emergent fitness asymmetry that favoured dispersal in low‐quality habitat. However, this initial dispersal advantage at low‐fitness RLs did not facilitate climate tracking, as it was outweighed by an increased probability of extinction. Locally adapted genotypes benefited from staying close to their climate optima; this selected against dispersal under stable climates but for increased dispersal throughout shifting ranges, compared to cases without local adaptation. Dispersal increased at expanding RLs in most scenarios, but only increased at the range centre and contracting RLs given local adaptation to climate.