Perspective: reverse evolution

Selection against domestication alleles in introduced rabbit populations

Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.

De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen

Bacteria evolving within human hosts encounter selective tradeoffs that render mutations adaptive in one context and deleterious in another. Here, we report that the cystic fibrosis-associated pathogen Burkholderia dolosa overcomes in-human selective tradeoffs by acquiring successive point mutations that alternate phenotypes. We sequenced the whole genomes of 931 respiratory isolates from two recently infected patients and an epidemiologically-linked, chronically-infected patient. These isolates are contextualized using 112 historical genomes from the same outbreak strain. Within both newly infected patients, diverse parallel mutations that disrupt O-antigen expression quickly arose, comprising 29% and 63% of their B. dolosa communities by 3 years. The selection for loss of O-antigen starkly contrasts with our previous observation of parallel O-antigen-restoring mutations after many years of chronic infection in the historical outbreak. Experimental characterization revealed that O-antigen loss increases uptake in immune cells while decreasing competitiveness in the mouse lung. We propose that the balance of these pressures, and thus whether O-antigen expression is advantageous, depends on tissue localization and infection duration. These results suggest that mutation-driven alternation during infection may be more frequent than appreciated and is underestimated without dense temporal sampling.

Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori

Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.

The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems

This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.

Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs

The dynamics of adaptation, reversion, and compensation have been central topics in microbial evolution, and several studies have attempted to resolve the population genetics underlying how these dynamics occur. However, questions remain regarding how certain features-the evolution of mutators and whether compensatory mutations alleviate costs fully or partially-may influence the evolutionary dynamics of compensation and reversion. In this study, we attempt to explain findings from experimental evolution by utilizing computational and theoretical approaches toward a more refined understanding of how mutation rate and the fitness effects of compensatory mutations influence adaptive dynamics. We find that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation is associated with a dramatically decreased probability of reversion to the wild type. These findings help to explain specific results from experimental evolution, where compensation was observed in nonmutator strains, but reversion (sometimes with compensation) was observed in mutator strains, indicating that real-world compensatory mutations are often unable to fully alleviate the costs associated with adaptation. Our findings emphasize the potential role of the supply and quality of mutations in crafting the dynamics of adaptation and reversal, with implications for theoretical population genetics and for biomedical contexts like the evolution of antibiotic resistance.

A mechanism of inheritance of acquired traits in animals

Observational and experimental evidence for the inheritance of acquired traits in animals is slowly, but steadily accumulating. The onset and transmission of acquired traits implies the acquisition and transmission from parents to progeny of new information, which is different from the genetic information contained in DNA. The new non-genetic information most commonly is passed on from parents to the offspring via gamete(s), but how it is precisely transmitted to the successive generations is still unknown. Based on adequate empirical evidence presented herein, a hypothesis is proposed of the inheritance of acquired traits in animals and the flow of the relevant parental information to the offspring.

Secondary Evolve and Resequencing: An Experimental Confirmation of Putative Selection Targets without Phenotyping

Evolve and resequencing (E&R) studies investigate the genomic responses of adaptation during experimental evolution. Because replicate populations evolve in the same controlled environment, consistent responses to selection across replicates are frequently used to identify reliable candidate regions that underlie adaptation to a new environment. However, recent work demonstrated that selection signatures can be restricted to one or a few replicate(s) only. These selection signatures frequently have weak statistical support, and given the difficulties of functional validation, additional evidence is needed before considering them as candidates for functional analysis. Here, we introduce an experimental procedure to validate candidate loci with weak or replicate-specific selection signature(s). Crossing an evolved population from a primary E&R experiment to the ancestral founder population reduces the frequency of candidate alleles that have reached a high frequency. We hypothesize that genuine selection targets will experience a repeatable frequency increase after the mixing with the ancestral founders if they are exposed to the same environment (secondary E&R experiment). Using this approach, we successfully validate two overlapping selection targets, which showed a mutually exclusive selection signature in a primary E&R experiment of Drosophila simulans adapting to a novel temperature regime. We conclude that secondary E&R experiments provide a reliable confirmation of selection signatures that either are not replicated or show only a low statistical significance in a primary E&R experiment unless epistatic interactions predominate. Such experiments are particularly helpful to prioritize candidate loci for time-consuming functional follow-up investigations.

Evolutionary History Drives Biogeographic Patterns of Coral Reef Resilience

Modern-day Indo-Pacific coral reefs are characterized by rapid recovery driven by pulses of coral recruitment, but Caribbean reefs exhibit low rates of recruitment and poor recovery following a wide range of disturbance events. The contrasting evolutionary history of coral taxa offers key insight into biogeographic patterns of coral resilience. Following the closure of the Isthmus of Panama approximately 2.8 million years ago, widespread extinction of Caribbean corals led to an evolutionary bottleneck that favored large and long-lived species with a relatively high reliance on asexual versus sexual reproduction. In contrast, adaptive radiation led to the evolution of superrecruiting tabular, digitate, and corymbose corals that drive the rapid recovery of modern-day Indo-Pacific reefs following disturbance. The dominance of branching growth forms and evolutionary absence of superrecruiting growth forms throughout the entire evolutionary history of the Caribbean (approximately 38 million years ago to present) may explain the exceptionally high recruitment rates on modern-day Indo-Pacific reefs and low historical recruitment on Caribbean reefs. The evolutionary history of the Caribbean coral reef-building taxa implies that, even with a reversal of ecosystem state, widespread recovery of Caribbean reefs may be limited.

Polygenic adaptation: a unifying framework to understand positive selection

Most adaption processes have a polygenic genetic basis, but even with the recent explosive growth of genomic data we are still lacking a unified framework describing the dynamics of selected alleles. Building on recent theoretical and empirical work we introduce the concept of adaptive architecture, which extends the genetic architecture of an adaptive trait by factors influencing its adaptive potential and population genetic principles. Because adaptation can be typically achieved by many different combinations of adaptive alleles (redundancy), we describe how two characteristics - heterogeneity among loci and non-parallelism between replicated populations - are hallmarks for the characterization of polygenic adaptation in evolving populations. We discuss how this unified framework can be applied to natural and experimental populations.

Increase in viability due to the accumulation of X chromosome mutations in Drosophila melanogaster males

To increase our understanding of the role of new X-chromosome mutations in adaptive evolution, single-X Drosophila melanogaster males were mated with attached-X chromosome females, allowing the male X chromosome to accumulate mutations over 28 generations. Contrary to our hypothesis that male viability would decrease over time, due to the accumulation and expression of X-linked recessive deleterious mutations in hemizygous males, viability significantly increased. This increase may be attributed to germinal selection and to new X-linked beneficial or compensatory mutations, possibly supporting the faster-X hypothesis.

Meiotic Genes in Colpodean Ciliates Support Secretive Sexuality

The putatively asexual Colpodean ciliates potentially pose a problem to macro-organismic theories of evolution. They are extremely ancient (although asexuality is thought to hasten extinction), and yet there is one apparently derived sexual species (implying an unlikely regain of a complex trait). If macro-organismic theories of evolution also broadly apply to microbial eukaryotes, though, then most or all of the colpodean ciliates should merely be secretively sexual. Here we show using de novo genome sequencing, that colpodean ciliates have the meiotic genes required for sex and these genes are under functional constraint. Along with these genomic data, we argue that these ciliates are sexual given the cytological observations of both micronuclei and macronuclei within their cells, and the behavioral observations of brief fusions as if the cells were mating. The challenge that colpodean ciliates pose is therefore not to evolutionary theory, but to our ability to induce microbial eukaryotic sex in the laboratory.

Genomics of Parallel Experimental Evolution in Drosophila

What are the genomic foundations of adaptation in sexual populations? We address this question using fitness–character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.

How could fully scaled carps appear in natural waters in Madagascar?

The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.

Epistasis and the Dynamics of Reversion in Molecular Evolution

Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time.

Cerebral cortex expansion and folding: what have we learned?

One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding. Cortical folding takes place during embryonic development and is important to optimize the functional organization and wiring of the brain, as well as to allow fitting a large cortex in a limited cranial volume. Pathological alterations in size or folding of the human cortex lead to severe intellectual disability and intractable epilepsy. Hence, cortical expansion and folding are viewed as key processes in mammalian brain development and evolution, ultimately leading to increased intellectual performance and, eventually, to the emergence of human cognition. Here, we provide an overview and discuss some of the most significant advances in our understanding of cortical expansion and folding over the last decades. These include discoveries in multiple and diverse disciplines, from cellular and molecular mechanisms regulating cortical development and neurogenesis, genetic mechanisms defining the patterns of cortical folds, the biomechanics of cortical growth and buckling, lessons from human disease, and how genetic evolution steered cortical size and folding during mammalian evolution.

Plastic and evolutionary responses to heat stress in a temperate dung fly: negative correlation between basal and induced heat tolerance?

Extreme weather events such as heat waves are becoming more frequent and intense. Populations can cope with elevated heat stress by evolving higher basal heat tolerance (evolutionary response) and/or stronger induced heat tolerance (plastic response). However, there is ongoing debate about whether basal and induced heat tolerance are negatively correlated and whether adaptive potential in heat tolerance is sufficient under ongoing climate warming. To evaluate the evolutionary potential of basal and induced heat tolerance, we performed experimental evolution on a temperate source population of the dung fly Sepsis punctum. Offspring of flies adapted to three thermal selection regimes (Hot, Cold and Reference) were subjected to acute heat stress after having been exposed to either a hot-acclimation or non-acclimation pretreatment. As different traits may respond differently to temperature stress, several physiological and life history traits were assessed. Condition dependence of the response was evaluated by exposing juveniles to different levels of developmental (food restriction/rearing density) stress. Heat knockdown times were highest, whereas acclimation effects were lowest in the Hot selection regime, indicating a negative association between basal and induced heat tolerance. However, survival, adult longevity, fecundity and fertility did not show such a pattern. Acclimation had positive effects in heat-shocked flies, but in the absence of heat stress hot-acclimated flies had reduced life spans relative to non-acclimated ones, thereby revealing a potential cost of acclimation. Moreover, body size positively affected heat tolerance and unstressed individuals were less prone to heat stress than stressed flies, offering support for energetic costs associated with heat tolerance. Overall, our results indicate that heat tolerance of temperate insects can evolve under rising temperatures, but this response could be limited by a negative relationship between basal and induced thermotolerance, and may involve some but not other fitness-related traits.

Reverse evolution leads to genotypic incompatibility despite functional and active site convergence

Understanding the extent to which enzyme evolution is reversible can shed light on the fundamental relationship between protein sequence, structure, and function. Here, we perform an experimental test of evolutionary reversibility using directed evolution from a phosphotriesterase to an arylesterase, and back, and examine the underlying molecular basis. We find that wild-type phosphotriesterase function could be restored (>10⁴-fold activity increase), but via an alternative set of mutations. The enzyme active site converged towards its original state, indicating evolutionary constraints imposed by catalytic requirements. We reveal that extensive epistasis prevents reversions and necessitates fixation of new mutations, leading to a functionally identical sequence. Many amino acid exchanges between the new and original enzyme are not tolerated, implying sequence incompatibility. Therefore, the evolution was phenotypically reversible but genotypically irreversible. Our study illustrates that the enzyme's adaptive landscape is highly rugged, and different functional sequences may constitute separate fitness peaks.

DOI:http://dx.doi.org/10.7554/eLife.06492.001

Enzymes in bacteria and other organisms are built following instructions contained within each cell's DNA. Changes in the DNA, that is to say, mutations, can alter the shape and activity of the enzymes that are produced, which can ultimately affect the ability of the organism to survive and reproduce. Mutations that are beneficial to the organism are more likely to be passed on to future generations, which can lead to populations changing over time.

The DNA sequences that an organism carries are referred to as its ‘genotype’ and the resulting physical characteristics of the organism are known as its ‘phenotype’. Studies of evolution tend to focus on how particular species or molecules become more different over time. However, one area that remains controversial is whether it is possible for evolution to be reversed so that an organism or molecule returns to a previous form.

An enzyme called PTE is said to have phosphotriesterase activity because it catalyzes this particular type of chemical reaction. Recently, a group of researchers used a method called ‘directed evolution’ to demonstrate that it is possible for PTE to evolve in a way that means it loses its phosphotriesterase activity and becomes able to catalyze a different type of chemical reaction. Here, Kaltenbach et al.—including some of the researchers from the previous work—investigated whether it was possible to use the same method to reverse this evolution and restore the enzyme's original activity.

The experiments show that reverse evolution is possible as phosphotriesterase activity was restored to the PTE enzyme from the previous study. However, although the phenotype of the final enzyme matched that of the original PTE enzyme, the genotypes did not match as the DNA sequences of the genes that encode these enzymes differ. The DNA does not revert to its original sequence because the effect of individual mutations on the phenotype depends on what other mutations are present. For example, as the enzyme evolved its new activity, additional mutations accumulated that did not alter enzyme activity. During the reverse evolution experiment, some of these mutations could have started to exert influence on the phenotype so that different mutations were required to restore the phosphotriesterase activity.

In the future, Kaltenbach et al.'s findings may aid efforts to engineer artificial enzymes for use in medicine or industry.

DOI:http://dx.doi.org/10.7554/eLife.06492.002

Laboratory selection quickly erases historical differentiation

The roles of history, chance and selection have long been debated in evolutionary biology. Though uniform selection is expected to lead to convergent evolution between populations, contrasting histories and chance events might prevent them from attaining the same adaptive state, rendering evolution somewhat unpredictable. The predictability of evolution has been supported by several studies documenting repeatable adaptive radiations and convergence in both nature and laboratory. However, other studies suggest divergence among populations adapting to the same environment. Despite the relevance of this issue, empirical data is lacking for real-time adaptation of sexual populations with deeply divergent histories and ample standing genetic variation across fitness-related traits. Here we analyse the real-time evolutionary dynamics of Drosophila subobscura populations, previously differentiated along the European cline, when colonizing a new common environment. By analysing several life-history, physiological and morphological traits, we show that populations quickly converge to the same adaptive state through different evolutionary paths. In contrast with other studies, all analysed traits fully converged regardless of their association with fitness. Selection was able to erase the signature of history in highly differentiated populations after just a short number of generations, leading to consistent patterns of convergent evolution.

Dipeptide analysis of p53 mutations and evolution of p53 family proteins

p53 gain-of-function mutations are similar to driver mutations in cancer genes, with both promoting tumorigenesis. Most previous studies focused on residues lost by mutations, providing information related to a dominantly-negative effect. However, to understand gain-of-function mutations, it is also important to investigate what are the distributions of residues gained by mutations. We compile available p53/p63/p73 protein sequences and construct a non-redundant dataset. We analyze the amino acid and dipeptide composition of p53/p63/p73 proteins across evolution and compare them with the gain/loss of amino acids and dipeptides in human p53 following cancer-related somatic mutations. We find that the ratios of amino acids gained via somatic mutations during evolution to those lost through p53 cancer mutations correlate with the ratios found in single nucleotide polymorphisms in the human proteome. The dipeptide mutational gain/loss ratios are inversely correlated with those observed over p53 evolution but tend to follow the increasing p63/p73-like dipeptide propensities. We successfully simulated the p53 cancer mutation spectrum using the dipeptide composition across the p53 family accounting for the likelihood of mutations in p53 codons. The results revealed that the p53 mutation spectrum is dominated not only by p53 evolution but also by reversal of evolution to a certain degree. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai.

Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila

Based on ecological and metabolic arguments, some authors predict that adaptation to novel, harsh environments should involve alleles showing negative (diminishing return) epistasis and/or that it should be mediated in part by evolution of maternal effects. Although the first prediction has been supported in microbes, there has been little experimental support for either prediction in multicellular eukaryotes. Here we use a line-cross design to study the genetic architecture of adaptation to chronic larval malnutrition in a population of Drosophila melanogaster that evolved on an extremely nutrient-poor larval food for 84 generations. We assayed three fitness-related traits (developmental rate, adult female weight and egg-to-adult viability) under the malnutrition conditions in 14 crosses between this selected population and a nonadapted control population originally derived from the same base population. All traits showed a pattern of negative epistasis between alleles improving performance under malnutrition. Furthermore, evolutionary changes in maternal traits accounted for half of the 68% increase in viability and for the whole of 8% reduction in adult female body weight in the selected population (relative to unselected controls). These results thus support both of the above predictions and point to the importance of nonadditive effects in adaptive microevolution.

The secondary loss of gyrencephaly as an example of evolutionary phenotypical reversal

Gyrencephaly (the folding of the surface of the neocortex) is a mammalian-specific trait present in almost all mammalian orders. Despite the widespread appearance of the trait, little is known about the mechanism of its genesis or its adaptive significance. Still, most of the hypotheses proposed concentrated on the pattern of connectivity of mature neurons as main components of gyri formation. Recent work on embryonic neurogenesis in several species of mammals revealed different progenitor and stem cells and their neurogenic potential as having important roles in the process of gyrification. Studies in the field of comparative neurogenesis revealed that gyrencephaly is an evolutionarily labile trait, and that some species underwent a secondary loss of a convoluted brain surface and thus reverted to a more ancient form, a less folded brain surface (lissencephaly). This phenotypic reversion provides an excellent system for understanding the phenomenon of secondary loss. In this review, we will outline the theory behind secondary loss and, as specific examples, present species that have undergone this transition with respect to neocortical folding. We will also discuss different possible pathways for obtaining (or losing) gyri. Finally, we will explore the potential adaptive consequence of gyrencephaly relative to lissencephaly and vice versa.

Estimating the rate of irreversibility in protein evolution

Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.

Genotypic but not phenotypic historical contingency revealed by viral experimental evolution

BACKGROUND

The importance of historical contingency in determining the potential of viral populations to evolve has been largely unappreciated. Identifying the constraints imposed by past adaptations is, however, of importance for understanding many questions in evolutionary biology, such as the evolution of host usage dynamics by multi-host viruses or the emergence of escape mutants that persist in the absence of antiviral treatments. To address this issue, we undertook an experimental approach in which sixty lineages of Tobacco etch potyvirus that differ in their past evolutionary history and degree of adaptation to Nicotiana tabacum were allowed to adapt to this host for 15 rounds of within host multiplication and transfer. We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage.

RESULTS

We found that past evolutionary history did not determine the phenotypic outcome of this common host evolution phase, and that the signal of local adaptation to past hosts had largely disappeared. By contrast, evolutionary history left footprints at the genotypic level, since the majority of host-specific mutations present at the beginning of this experiment were retained in the end-point populations and may have affected which new mutations were consequently fixed. This resulted in further divergence between the sequences despite a shared selective environment.

CONCLUSIONS

The present experiment reinforces the idea that the answer to the question "How important is historical contingency in evolution?" strongly depends on the level of integration of the traits studied. A strong historical contingency was found for TEV genotype, whereas a weak effect of on phenotypic evolution was revealed. In an applied context, our results imply that viruses are not easily trapped into suboptimal phenotypes and that (re)emergence is not evolutionarily constrained.

The yield of experimental yeast populations declines during selection

The trade-off between growth rate and yield can limit population productivity. Here we tested for this life-history trade-off in replicate haploid and diploid populations of Saccharomyces cerevisiae propagated in glucose-limited medium in batch cultures for 5000 generations. The yield of single clones isolated from the haploid lineages, measured as both optical and population density at the end of a growth cycle, declined during selection and was negatively correlated with growth rate. Initially, diploid populations did not pay this cost of adaptation but haploidized after about 1000-3000 generations of selection, and this ploidy transition was associated with a decline in yield caused by reduced cell size. These results demonstrate the experimental evolution of a trade-off between growth rate and yield, caused by antagonistic pleiotropy, during adaptation in haploids and after an adaptive transition from diploidy to haploidy.

New experiments for an undivided genetics

There used to be a broad split within the experimental genetics research community between those who did mechanistic research using homozygous laboratory strains and those who studied patterns of genetic variation in wild populations. The former benefited from the advantage of reproducible experiments, but faced difficulties of interpretation given possible genomic and evolutionary complexities. The latter research approach featured readily interpreted evolutionary and genomic contexts, particularly phylogeny, but was poor at determining functional significance. Such burgeoning experimental strategies as genome-wide analysis of quantitative trait loci, genotype-phenotype associations, and the products of experimental evolution are now fostering a unification of experimental genetic research that strengthens its scientific power.

Re-establishment of biting mouthparts in desert-living dung beetles (Scarabaeidae: Scarabaeinae) feeding on plant litter-Old structures reacquired or new ones evolved?

Evolution of mouthparts in adult dung beetles (Scarabaeidae: Scarabaeinae) for eating moist, fresh dung was linked with a loss of the ability to chew. However, the desert-living genus Pachysoma, probably evolved from a wet-dung feeding, Scarabaeus-like ancestor, has switched to a diet of dry fecal pellets (of rodents or small ruminants) and plant litter that requires re-establishment of chewing. Indeed, gut contents of a litter-feeding Pachysoma species indicate efficient food comminution. Based on scanning electron microscopy, cutting and grinding mouthpart structures in six Pachysoma species, of two lineages and with different food preferences, are described and compared with homologous structures in wet-dung feeding Scarabaeus species. In Pachysoma, cutting and breaking of large food items is probably performed by a clypeal scraper, a prominent epipharyngeal tooth and large maxillary galeal hooks. Further comminution is achieved by a large, grinding area evolved on the mandibular molae. Interspecific differences and the probable function and evolution of these structures are discussed. Particularly, the unique tools for cutting/breaking are completely novel structures and not results of some reacquisition of normal biting mouthparts.

Fitness recovery and compensatory evolution in natural mutant lines of C. elegans

Deleterious mutation accumulation plays a central role in evolutionary genetics, conservation biology, human health, and evolutionary medicine (e.g., methods of viral attenuation for live vaccines). It is therefore important to understand whether and how quickly populations with accumulated deleterious mutational loads can recover fitness through adaptive evolution. We used laboratory experimental evolution with four long-term mutation-accumulation (MA) lines of Caenorhabditis elegans nematodes to study the dynamics of such fitness evolution. We previously showed that when homozygous mutant populations are evolved in large population sizes, they can rapidly achieve wild-type fitness through the accumulation of new beneficial or compensatory epistatic mutations. Here, we expand this approach to demonstrate that when replicate lineages are initiated from the same mutant genotype, phenotypic evolution is only sometimes repeatable. MA genotypes that recovered ancestral fitness in the previous experiment did not always do so here. Further, the pattern of adaptive evolution in independently evolved replicates was contingent upon the MA genotype and varied among fitness-related traits. Our findings suggest that new beneficial mutations can drive rapid fitness evolution, but that the adaptive process is rendered somewhat unpredictable by its susceptibility to chance events and sensitivity to the evolutionary history of the starting population.

Uner tan syndrome: history, clinical evaluations, genetics, and the dynamics of human quadrupedalism

This review includes for the first time a dynamical systems analysis of human quadrupedalism in Uner Tan syndrome, which is characterized by habitual quadrupedalism, impaired intelligence, and rudimentary speech. The first family was discovered in a small village near Iskenderun, and families were later found in Adana and two other small villages near Gaziantep and Canakkale. In all the affected individuals dynamic balance was impaired during upright walking, and they habitually preferred walking on all four extremities. MRI scans showed inferior cerebellovermian hypoplasia with slightly simplified cerebral gyri in three of the families, but appeared normal in the fourth. PET scans showed a decreased glucose metabolic activity in the cerebellum, vermis and, to a lesser extent the cerebral cortex, except for one patient, whose MRI scan also appeared to be normal. All four families had consanguineous marriages in their pedigrees, suggesting autosomal recessive transmission. The syndrome was genetically heterogeneous. Since the initial discoveries more cases have been found, and these exhibit facultative quadrupedal locomotion, and in one case, late childhood onset. It has been suggested that the human quadrupedalism may, at least, be a phenotypic example of reverse evolution. From the viewpoint of dynamic systems theory, it was concluded there may not be a single factor that predetermines human quadrupedalism in Uner Tan syndrome, but that it may involve self-organization, brain plasticity, and rewiring, from the many decentralized and local interactions among neuronal, genetic, and environmental subsystems.

Secretive ciliates and putative asexuality in microbial eukaryotes

Facultative sexuality is assumed to have occurred in the ancestor of all extant eukaryotes, but the distribution and maintenance of sex among microbial eukaryotes is still under debate. In this paper, we address the purported asexuality in colpodean ciliates as an exemplary lineage. Colpodeans are a primarily terrestrial clade thought to have arisen up to 900 MYA and contain one known derived sexual species. We conclude that the putative asexuality of this lineage is an observational artifact. We suggest that the same might hold for other microbial eukaryotes, and that many are secretively sexual as well. Theoretical work from the distantly related plants and animals suggests that both the evolutionary success of ancient asexuals and the reversal of the loss of sex are highly unlikely, further suggesting that colpodeans are secretively sexual. However, it remains to be seen to what extent sexual theories and predictions derived from macro-organismic lineages apply also to microbial eukaryotes.

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

The extent to which evolution is reversible has long fascinated biologists. Most previous work on the reversibility of morphological and life-history evolution has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters. Further, despite theoretical work on the factors that could contribute to irreversibility, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent 'restrictive' mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes

Two fundamental life cycle types are recognized among hydrozoan cnidarians, the benthic (generally colonial) polyp stage either producing pelagic sexual medusae or directly releasing gametes elaborated from an attached gonophore. The existence of intermediate forms, with polyps producing simple medusoids, has been classically considered compelling evidence in favor of phyletic gradualism. In order to gain insights about the evolution of hydrozoan life history traits, we inferred phylogenetic relationships of 142 species of Thecata (= Leptothecata, Leptomedusae), the most species-rich hydrozoan group, using 3 different ribosomal RNA markers (16S, 18S, and 28S). In conflict with morphology-derived classifications, most thecate species fell in 2 well-supported clades named here Statocysta and Macrocolonia. We inferred many independent medusa losses among Statocysta. Several instances of secondary regain of medusoids (but not of full medusa) from medusa-less ancestors were supported among Macrocolonia. Furthermore, life cycle character changes were significantly correlated with changes affecting colony shape. For both traits, changes did not reflect graded and progressive loss or gain of complexity. They were concentrated in recent branches, with intermediate character states being relatively short lived at a large evolutionary scale. This punctuational pattern supports the existence of 2 alternative stable evolutionary strategies: simple stolonal colonies with medusae (the ancestral strategy, seen in most Statocysta species) versus large complex colonies with fixed gonophores (the derived strategy, seen in most Macrocolonia species). Hypotheses of species selection are proposed to explain the apparent long-term stability of these life history traits despite a high frequency of character change. Notably, maintenance of the medusa across geological time in Statocysta might be due to higher extinction rates for species that have lost this dispersive stage.

Loss of evolutionary resistance by the oligochaete Limnodrilus hoffmeisteri to a toxic substance--cost or gene flow?

The oligochaete Limnodrilus hoffmeisteri at Foundry Cove (FC), New York evolved genetic resistance to cadmium (Cd) and lost resistance after contaminated sediments were removed by dredging. Selection (on survival time in dissolved Cd) was used to generate tolerance to evaluate fitness cost, the commonplace expectation for evolutionary reversal. The hypothesis that gene flow from neighboring populations could "swamp" resistance was addressed by 16S rDNA sequences. In disagreement with the cost hypothesis, selected-Cd tolerant worms and controls showed no difference in total fecundity or growth rate in environments. Highly-Cd-tolerant worms of the FC-selected population grew rapidly at different temperatures and showed no growth impairment in the presence of Cd, indicating metabolically efficient resistance. Genetic structure at FC was consistent with invasion of genotypes from an adjacent population in the time since dredging. Applying selection to lines from FC and a reference site, demonstrated a more rapid increase in Cd tolerance in FC-origin lines, indicating standing allelic variation for resistance at FC (despite phenotypic erosion). The selection experiment supports the view that resistance is simply controlled--probably by one allele of large effect. Whether such rapid "readaptation" could occur naturally is an important question for understanding broad effects of pollutants.

A WRIST-WALKER EXHIBITING NO “UNER TAN SYDNROME”: A THEORY FOR POSSIBLE MECHANISMS OF HUMAN DEVOLUTION TOWARD THE ATAVISTIC WALKING PATTERNS

After discovering two families with handicapped children exhibiting the "Uner Tan syndrome," the author discovered a man exhibiting only wrist-walking with no primitive mental abilities including language. According to his mother, he had an infectious disease with high fever as a three months old baby; as a result, the left leg had been paralyzed after a penicilline injection. This paralysis most probably resulted from a viral disease, possibly poliomyelitis. He is now (2006) 36 years old; the left leg is flaccid and atrophic, with no tendon reflexes; however, sensation is normal. The boy never stood up on his feet while maturing. The father forced him to walk upright using physical devices and making due exercises, but the child always rejected standing upright and walking in erect posture; he always preferred wrist-walking; he expresses that wrist-walking is much more comfortable for him than upright-walking. He is very strong now, making daily body building exercises, and walking quite fast using a "three legs," although he cannot stand upright. Mental status, including the language and conscious experience, is quite normal. There was no intra-familiar marriage as in the two families mentioned earlier, and there is no wrist-walking in his family and relatives. There were no cerebellar signs and symptoms upon neurological examination. The brain-MRI was normal; there was no atrophy in cerebellum and vermis. It was concluded that there may be sporadic wrist-walkers exhibiting no "Uner Tan Syndrome." The results suggest that the cerebellum has nothing to do with human wrist-walking, which may rather be an atavistic trait appearing from time to time in normal individuals, indicating a live model for human reverse evolution. It was concluded that pure quadrupeds may sporadically appear due to random fluctuations in genotypes and/or environmental factors (hormonal or nutritional); the human development following the human evolution may be stopped in the stage of transition from quadrupedality to bipedality. That is, the activity of the philogenetically youngest supraspinal centers for bipedal walking responsible for suppression of the older supraspinal centers for quadrupedal gait may be interrupted at the atavistic level due to genetic and/or environmental factors. Consequently, it is assumed that these individuals prefer their natural wrist-walking to move around more quickly and efficiently.

Reverse evolution of armor plates in the threespine stickleback

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution,"[9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime.

Unertan syndrome: review and report of four new cases

The aim of this study was to describe additional patients (n= 3) exhibiting the Unertan syndrome (UTS), resident in rural areas of Canakkale. The 8th and 9th families with the UTS, with a total of 16 members affected, have not been previously characterized. A single, non-familial case (Bayramic, Canakkale) occurred during early childhood after an infection with a high fever. Three cases of familial UTS were located in another village in Canakkale. All cases exhibited the three key symptoms of the UTS: (1) walking on all four extremities, (2) primitive language (only sounds), and (3) rudimentary intelligence. Magnetic resonance imaging showed mild vermial hypoplasia in the non-familial case, while there was cerebellar and vermial hypoplasia with a flattened cerebral cortex in the familial cases. Dexterity of the fingers was normal. The man from the latter family was fond of dragging a wooden box after fastening a string around his belt. The collective observations and clinical findings suggest two etiologies for the UTS: (1) genetic, via autosomal recessive transmission and (2) viral, likely the poliovirus affecting the cerebro-cerebellar structures. At a minimum, vermial hypoplasia is suggested to cause fully developed UTS. The subjects could stand upright and even walk bipedally, despite difficulties in balance (ataxia), but they preferred quadrupedal walking. The main difficulty with gait was maintaining a dynamic-asymmetric lateral balance and initiation of the first step during standing. Apparently, a quadrupedal gait in an adult is a developmental regression with absence of the higher control mechanisms for asymmetric lateral balance during bipedal walking. It is suggested that these individuals exhibit ancestral traits; the quadrupedal gait with rudimentary intelligence and primitive speech resulting from viral infections and/or genetic damage may cause devolution (reverse evolution), a manifestation of an experiment of nature as well as experimental studies in animal models. The results support the notion of punctuated evolution, in contrast to Darwin's theory of graded evolution. Dragging a wooden box using a string wrapped around the belt may also be an example of reverse evolution with regard to tool making, illuminating the very long-lasting period before the invention of the wheel. Herein, there has been no intent to insult or injure these individuals affected by the UTS; rather, this is an endeavor to better understand the mystery of human evolution. Go to the publisher's online edition of International Journal of Neuroscience for the following free supplemental resource: video clips.

Unertan syndrome: a case series demonstrating human devolution

A large family with six individuals exhibiting the Unertan syndrome (UTS) was identified residing in southern Turkey. All of the individuals had mental impairments and walked on all four extremities. The practice of intra-familial marriages suggested that the UTS may be an autosomal recessive disorder, similar to previously described cases. The inferior portions of the cerebellum and vermis were absent as evidenced by MRI and CT scans. The height and head circumference of those affected were within normal ranges. Barany's test suggested normal vestibular system function. The subjects could not name objects or their close relatives. The males (n = 4) could understand simple questions and commands, but answered questions with only one or two sounds. The females (n = 2) were superior to the males with respect to language skills and walking, suggesting an association between walking and speaking abilities. One male exhibited three walking patterns at the same time: quadripedal, tiptoe, and scissor walking. Another male used two walking styles: quadripedal and toe-walking. It is emphasized that there are important differences between the UTS and the disequilibrium syndrome. It is suggested that the inability to walk upright in those affected with the UTS may be best explained by a disturbance in lateral-balance mechanisms, without being related to the cerebello-vestibular system. An interruption of locomotor development during the transition from quadripedality to bipedality may result in habitual walking on all four extremities and is normal in some children. Because quadripedal gait is an ancestral trait, individuals with the UTS, exhibiting a manifestation of reverse evolution in humans, may be considered an experiment of nature, useful in understanding the mechanisms underlying the transition from quadripedality to bipedality during human evolution. The proposed mutant gene or gene pool playing a role in human quadrupedality may also be responsible for human bipedality at the same time. Herein there is no intent to insult or injure; rather, this report is an endeavor to better understand human beings. Supplementary materials are available for this article. Go to the publisher's online edition of International Journal of Neuroscience for the following free supplemental resource(s): video clips.