Weak selection and protein evolution

The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.     

Reverse evolution: selection against costly resistance in disease-free microcosm populations of Paramecium caudatum

Evolutionary costs of parasite resistance arise if genes conferring resistance reduce fitness in the absence of parasites. Thus, parasite-mediated selection may lead to increased resistance and a correlated decrease in fitness, whereas relaxed parasite-mediated selection may lead to reverse evolution of increased fitness and a correlated decrease in resistance. We tested this idea in experimental populations of the protozoan Paramecium caudatum and the parasitic bacterium Holospora undulata. After eight years, resistance to infection and asexual reproduction were compared among paramecia from (1) "infected" populations, (2) uninfected "naive" populations, and (3) previously infected, parasite-free "recovered" populations. Paramecia from "infected" populations were more resistant (+12%), but had lower reproduction (-15%) than "naive" paramecia, indicating an evolutionary trade-off between resistance and fitness. Recovered populations showed similar reproduction to naive populations; however, resistance of recently (<3 years) recovered populations was similar to paramecia from infected populations, whereas longer (>3 years) recovered populations were as susceptible as naive populations. This suggests a weak, convex trade-off between resistance and fitness, allowing recovery of fitness, without complete loss of resistance, favoring the maintenance of a generalist strategy of intermediate fitness and resistance. Our results indicate that (co)evolution with parasites can leave a genetic signature in disease-free populations.     

Geographical variation in growth form traits in Quercus suber and its relation to population evolutionary history

Differential selection pressures caused by environmental disparities lead to populations to become differentiated as they adapt to local environments. In addition, natural selection during the species past can contribute to the observed differentiation. In this study, we examine the geographic variation in a set of four traits related to growth and plant architecture in cork oak (Quercus suber) and investigate to what extent this variation is the result of the effects of ongoing evolution in current environments and the past evolutionary history of the species. Cork oak saplings at the common garden trial exhibited differences in plant architecture associated to cpDNA lineage. Eastern lineages, exhibited the lowest apical dominance and highest branchiness, consistent with the analyses in other cork oak trials. In contrast, patterns linked to the evolutionary past were less evident in height and diameter. These results suggest that selective pressures after cpDNA divergence can have blurred patterns in some traits closely related to fitness, while conserving the past evolutionary imprints in plant architectural traits. Introgressed populations did not show significant differentiation in architecture, which suggests that allele exchanges via hybridization have had a limited effect on population differentiation in cork oak. Finally, populations within lineages also showed differences in growth and architecture. Correlation between population architecture and temperature patterns were observed indicating that environmental factors such as climate also could result crucial in the evolution of plant architecture of cork oak within lineages.     

Evolutionary responses to global change: lessons from invasive species

Biologists have recently devoted increasing attention to the role of rapid evolution in species' responses to environmental change. However, it is still unclear what evolutionary responses should be expected, at what rates, and whether evolution will save populations at risk of extinction. The potential of biological invasions to provide useful insights has barely been realised, despite the close analogies to species responding to global change, particularly climate change; in both cases, populations encounter novel climatic and biotic selection pressures, with expected evolutionary responses occurring over similar timescales. However, the analogy is not perfect, and invasive species are perhaps best used as an upper bound on expected change. In this article, we review what invasive species can and cannot teach us about likely evolutionary responses to global change and the constraints on those responses. We also discuss the limitations of invasive species as a model and outline directions for future research.     

Molecular hyperdiversity and evolution in very large populations

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro‐evolutionary selective pressures on noncoding regulatory elements.     

The neutral theory of molecular evolution and the world view of the neutralists

The main tenet of the neutral theory is that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random fixation of selectively neutral (or very nearly neutral) alleles through random sampling drift under continued mutation pressure. The theory also asserts that the majority of protein and DNA polymorphisms are selectively neutral, and that they are maintained in the species by mutational input balanced by random extinction rather than by "balancing selection." The neutral theory is based on simple assumptions. This enabled us to develop mathematical theories (using the diffusion equation method) that can treat these phenomena in quantitative terms and that permit theory to be tested against actual observations. Although the neutral theory has been severely criticized by the neo-Darwinian establishment, supporting evidence has accumulated over the last 20 years. In particular, the recent burst of DNA sequence data helped to strengthen the theory a great deal. I believe that the neutral theory triggered reexamination of the traditional "synthetic theory of evolution." In this paper, I review the present status of the neutral theory, including discussions of such topics as "molecular evolutionary clock," very high evolutionary rates observed in RNA viruses, a deviant coding system found in Mycoplasm together with the concept of mutation-driven neutral evolution, and the origin of life. I also present a worldview based on the conception of what I call "survival of the luckiest."     

History repeats itself: genomic divergence in copepods

Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the tape would lead evolution down a pathway radically different from the road actually taken (Gould 1989). This thought experiment has puzzled evolutionary biologists for a long time: how repeatable are evolutionary events? And if history does indeed repeat itself, what are the factors that may help us predict the path taken? A powerful means to address these questions at a small evolutionary scale is to study closely related populations that have evolved independently, under similar environmental conditions. This is precisely what Pereira et al. ( 2016 ) set out to do using marine copepods Tigriopus californicus, and present their results in this issue of Molecular Ecology. They show that evolution can be repeatable and even partly predictable, at least at the molecular level. As expected from theory, patterns of divergence were shaped by natural selection. At the same time, strong genetic drift due to small population sizes also constrained evolution down a similar evolutionary road, and probably contributed to repeatable patterns of genomic divergence.     

Evolutionary biotechnology – theory,facts and perspectives

Molecular evolution has recently been applied in biotechnology which consist of the development of evolutionary strategies in the design of biopolymers with predefined properties and functions. At the heart of this new technology are the in vitro replication and random synthesis of RNA or DNA molecules, producing large libraries of genotypes that are subjected to selection techniques following DARWIN's principle. By means of these evolutionary methods, RNA molecules were derived which specifically bind to predefined target molecules. Ribozymes with new catalytic functions were obtained as well as RNA molecules that are resistant to cleavage by specific RNases. In addition, the catalytic specificities of group I introns, a special class of ribozymes, were modified by variation and selection. Efficient applications of molecular evolution to problems in biotechnology require a fundamental and detailed understanding of the evolutionary process. Two basic questions are of primary importance: (i) How can evolutionary methods be successful as the numbers of possible genotypes are so large that the chance of obtaining a particular sequence by random processes is practically zero, and (ii) how can populations avoid being caught in evolutionary traps corresponding to local fitness optima? This review is therefore concerned with an abridged account of the theory of molecular evolution, as well as its application to biotechnology. We add a brief discussion of new techniques for the massively parallel handling and screening of very small probes as is required for the spatial separation and selection of genotypes. Finally, some imminent prospects concerning the evolutionary design of biopolymers are presented.     

Analyses of physiological evolutionary response

Selection studies are useful if they can provide us with insights into the patterns and processes of evolution in populations under controlled conditions. In this context it is particularly valuable to be able to analyze the limitations of and constraints on evolutionary responses to allow predictions concerning evolutionary change. The concept of a selection pathway is presented as a means of visualizing this predictive process and the constraints that help define the population's response to selection. As pointed out by Gould and Lewontin, history and chance are confounding forces that can mask or distort the adaptive response. Students of the evolutionary responses of organisms are very interested in the effects of these confounding forces, since they play a critical role not only in the laboratory but also in natural selection in the field. In this article, we describe some methods that are a bit different from those used in most studies for examining data from laboratory selection studies. These analytical methods are intended to provide insights into the physiological mechanisms by which evolutionary responses to the environment proceed. Interestingly, selection studies often exhibit disparate responses in replicate populations. We offer methods for analyzing these disparate responses in replicate populations to better understand this very important source of variability in the evolutionary response. We review the techniques of Travisano et al. and show that these approaches can be used to investigate the relative roles of adaptation, history, and chance in the evolutionary responses of populations of Drosophila melanogaster to selection for enhanced desiccation resistance. We anticipate that a wider application of these techniques will provide valuable insights into the organismal, genetic, and molecular nature of the constraints, as well as the factors that serve to enhance or, conversely, to mask the effects of chance. Such studies should help to provide a more detailed understanding of the processes producing evolutionary change in populations.     

Self-structuring in spatial evolutionary ecology

Spatial self-structuring has been a focus of recent interest among evolutionary ecologists. We review recent developments in the study of the interplay between spatial self-structuring and evolution. We first discuss the relative merits of the various theoretical approaches to spatial modelling in ecology. Second, we synthesize the main theoretical studies of the evolution of cooperation in spatially structured populations. We show that population viscosity is generally beneficial to cooperation, because cooperators can reap additional benefits from being clustered. A similar mechanism can explain the evolution of honest communication and of reduced virulence in host–parasite interactions. We also discuss some recent innovative empirical results that test these theories. Third, we show the relevance of these results to the general field of evolutionary ecology. An important conclusion is that kin selection is the main process that drives evolution of cooperation in viscous populations. Many results of kin selection theory can be recovered as emergent properties of spatial ecological dynamics. We discuss the implications of these results for the study of multilevel selection and evolutionary transitions. We conclude by sketching some perspectives for future research, with a particular emphasis on the topics of evolutionary branching, criticality, spatial fluctuations and experimental tests of theoretical predictions.     

What have two decades of laboratory life-history evolution studies onDrosophila melanogaster taught us?

A series of laboratory selection experiments onDrosophila melanogaster over the past two decades has provided insights into the specifics of life-history tradeoffs in the species and greatly refined our understanding of how ecology and genetics interact in life-history evolution. Much of what has been learnt from these studies about the subtlety of the microevolutionary process also has significant implications for experimental design and inference in organismal biology beyond life-history evolution, as well as for studies of evolution in the wild. Here we review work on the ecology and evolution of life-histories in laboratory populations ofD. melanogaster, emphasizing how environmental effects on life-history-related traits can influence evolutionary change. We discuss life-history tradeoffs—many unexpected—revealed by selection experiments, and also highlight recent work that underscores the importance to life-history evolution of cross-generation and cross-life-stage effects and interactions, sexual antagonism and sexual dimorphism, population dynamics, and the possible role of biological clocks in timing life-history events. Finally, we discuss some of the limitations of typical selection experiments, and how these limitations might be transcended in the future by a combination of more elaborate and realistic selection experiments, developmental evolutionary biology, and the emerging discipline of phenomics.     

Detecting the molecular signature of social conflict: theory and a test with bacterial quorum sensing genes

Extending social evolution theory to the molecular level opens the door to an unparalleled abundance of data and statistical tools for testing alternative hypotheses about the long-term evolutionary dynamics of cooperation and conflict. To this end, we take a collection of known sociality genes (bacterial quorum sensing [QS] genes), model their evolution in terms of patterns that are detectable using gene sequence data, and then test model predictions using available genetic data sets. Specifically, we test two alternative hypotheses of social conflict: (1) the "adaptive" hypothesis that cheaters are maintained in natural populations by frequency-dependent balancing selection as an evolutionarily stable strategy and (2) the "evolutionary null" hypothesis that cheaters are opposed by purifying kin selection yet exist transiently because of their recurrent introduction into populations by mutation (i.e., kin selection-mutation balance). We find that QS genes have elevated within- and among-species sequence variation, nonsignificant signatures of natural selection, and putatively small effect sizes of mutant alleles, all patterns predicted by our evolutionary null model but not by the stable cheater hypothesis. These empirical findings support our theoretical prediction that QS genes experience relaxed selection due to nonclonality of social groups, conditional expression, and the individual-level advantage enjoyed by cheaters. Furthermore, cheaters are evolutionarily transient, persisting in populations because of their recurrent introduction by mutation and not because they enjoy a frequency-dependent fitness advantage.     

The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies

First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.     

The tragedy of the commons in microbial populations: insights from theoretical, comparative and experimental studies

First principles of thermodynamics imply that metabolic pathways are faced with a trade-off between the rate and yield of ATP production. Simple evolutionary models argue that this trade-off generates a fundamental social conflict in microbial populations: average fitness in a population is highest if all individuals exploit common resources efficiently, but individual reproductive rate is maximized by consuming common resources at the highest possible rate, a scenario known as the tragedy of the commons. In this paper, I review studies that have addressed two key questions: What is the evidence that the rate-yield trade-off is an evolutionary constraint on metabolic pathways? And, if so, what determines evolutionary outcome of the conflicts generated by this trade-off? Comparative studies and microbial experiments provide evidence that the rate-yield trade-off is an evolutionary constraint that is driven by thermodynamic constraints that are common to all metabolic pathways and pathway-specific constraints that reflect the evolutionary history of populations. Microbial selection experiments show that the evolutionary consequences of this trade-off depend on both kin selection and biochemical constraints. In well-mixed populations with low relatedness, genotypes with rapid and efficient metabolism can coexist as a result of negative frequency-dependent selection generated by density-dependent biochemical costs of rapid metabolism. Kin selection can promote the maintenance of efficient metabolism in structured populations with high relatedness by ensuring that genotypes with efficient metabolic pathways gain an indirect fitness benefit from their competitive restraint. I conclude by suggesting avenues for future research and by discussing the broader implications of this work for microbial social evolution.     

Rapid genome‐wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome‐wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late‐season drought in California. These ancestor‐descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (F_ST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome‐wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution.     

Morphological differentiation and genetic structure in island lizard populations

Only some island populations of Podarcis sicula are hyperchromatic. The study of this phenomenon and its relationship with the lizards of the mainland and other islands, exhibiting a "normal" coloration, provides useful hints in our understanding of evolutionary mechanisms that have created the observed morphological variation. We performed a comparative morphological and genetic analysis of a hyperchromatic lizard population from Licosa Island, and compared the data with that obtained from normal-colored lizard populations both from Ustica and Cirella islands in the Tyrrhenian sea and from nearby mainland Italy. Morphological and microsatellite gene differentiation in the hyperchromatic Licosa population appears to have been much more rapid than the molecular evolution of the mtDNA. We discuss herein that the comparison of hyperchromatism and other types of morphological variation with molecular data in island populations of lizards may provide useful hints as to evolutionary mechanisms.     

From genotype to phenotype: buffering mechanisms and the storage of genetic information

DNA sequence variation is abundant in wild populations. While molecular biologists use genetically homogeneous strains of model organisms to avoid this variation, evolutionary biologists embrace genetic variation as the material of evolution since heritable differences in fitness drive evolutionary change. Yet, the relationship between the phenotypic variation affecting fitness and the genotypic variation producing it is complex. Genetic buffering mechanisms modify this relationship by concealing the effects of genetic and environmental variation on phenotype. Genetic buffering allows the build-up and storage of genetic variation in phenotypically normal populations. When buffering breaks down, thresholds governing the expression of previously silent variation are crossed. At these thresholds, phenotypic differences suddenly appear and are available for selection. Thus, buffering mechanisms modulate evolution and regulate a balance between evolutionary stasis and change. Recent work provides a glimpse of the molecular details governing some types of genetic buffering.     

The pace of modern life II: from rates of contemporary microevolution to pattern and process

We compiled a database of microevolution on contemporary time scales in nature (47 source articles; 30 animal species), comprising 2649 evolutionary rates in darwins (proportional change per million years) and 2151 evolutionary rates in haldanes (standard deviations per generation). Here we demonstrate how quantitative rate measures can provide general insights into patterns and processes of evolution. The frequency distribution of evolutionary rates was approximately log-normal, with many slow rates and few fast rates. Net selection intensities estimated from haldanes were on average lower than selection intensities commonly measured directly in natural populations. This difference suggests that natural selection could easily accomplish observed microevolution but that the intensities of selection typically measured in nature are rarely maintained for long (otherwise observed evolutionary rates would be higher). Traits closely associated with fitness (life history traits) appear to evolve at least as fast as traits less closely tied to fitness (morphology). The magnitude of evolutionary difference increased with the length of the time interval, particularly when maximum rates from a given study were considered. This pattern suggests a general underlying tendency toward increasing evolutionary diversification with time. However, evolutionary rates also tended to decrease with time, perhaps because longer time intervals average increasingly disparate rates over time, or because evolution slows when populations approach new optima or as genetic variation is depleted. In combination, our results suggest that macroevolutionary transitions may ultimately arise through microevolution occasionally writ large but are perhaps temporally characterized by microevolution writ in fits and starts.     

Ecological rigidity and the hardness of selection in the wild

Hutchinson's ecological theater and evolutionary play is a classical view of evolutionary ecology—ecology provides a template in which evolution occurs. An opposing view is that ecological and evolutionary changes are like two actors on a stage, intertwined by density and frequency dependence. These opposing views correspond to hard and soft selection, respectively. Although often presented as diametrically opposed, both types of selection can occur simultaneously, yet we largely lack knowledge of the relative importance of hard versus soft selection in the wild. I use a dataset of 3000 individual gall makers from 15 wild local populations over 5 years to investigate the hardness of selection. I show that enemy attack consistently favors some gall sizes over others (hard selection) but that these biases can be fine-tuned by density and frequency dependence (soft selection). As a result, selection is hard and soft in roughly equal measures, but the importance of each type varies as species interactions shift. I conclude that eco-evolutionary dynamics should occur when a mix of hard and soft selection acts on a population. This work contributes to the rapprochement of disparate views of evolutionary ecology—ecology is neither a rigid theater nor a flexible actor, but instead embodies components of both.     

Are There Laws of Genome Evolution?

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.