Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation.

Modeling the rate at which adaptive phenotypes appear in a population is a key to predicting evolutionary processes. Given random mutations, should this rate be modeled by a simple Poisson process, or is a more complex dynamics needed? Here we use analytic calculations and simulations of evolving populations on explicit genotype-phenotype maps to show that the introduction of novel phenotypes can be "bursty" or overdispersed. In other words, a novel phenotype either appears multiple times in quick succession or not at all for many generations. These bursts are fundamentally caused by statistical fluctuations and other structure in the map from genotypes to phenotypes. Their strength depends on population parameters, being highest for "monomorphic" populations with low mutation rates. They can also be enhanced by additional inhomogeneities in the mapping from genotypes to phenotypes. We mainly investigate the effect of bursts using the well-studied genotype-phenotype map for RNA secondary structure, but find similar behavior in a lattice protein model and in Richard Dawkins's biomorphs model of morphological development. Bursts can profoundly affect adaptive dynamics. Most notably, they imply that fitness differences play a smaller role in determining which phenotype fixes than would be the case for a Poisson process without bursts.

Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.

Biomorphs, Richard Dawkins's iconic model of morphological evolution, are traditionally used to demonstrate the power of natural selection to generate biological order from random mutations. Here we show that biomorphs can also be used to illustrate how developmental bias shapes adaptive evolutionary outcomes. In particular, we find that biomorphs exhibit phenotype bias, a type of developmental bias where certain phenotypes can be many orders of magnitude more likely than others to appear through random mutations. Moreover, this bias exhibits a strong preference for simpler phenotypes with low descriptional complexity. Such bias towards simplicity is formalised by an information-theoretic principle that can be intuitively understood from a picture of evolution randomly searching in the space of algorithms. By using population genetics simulations, we demonstrate how moderately adaptive phenotypic variation that appears more frequently upon random mutations can fix at the expense of more highly adaptive biomorph phenotypes that are less frequent. This result, as well as many other patterns found in the structure of variation for the biomorphs, such as high mutational robustness and a positive correlation between phenotype evolvability and robustness, closely resemble findings in molecular genotype-phenotype maps. Many of these patterns can be explained with an analytic model based on constrained and unconstrained sections of the genome. We postulate that the phenotype bias towards simplicity and other patterns biomorphs share with molecular genotype-phenotype maps may hold more widely for developmental systems.

A toxic environment selects for specialist microbiome in poison frogs.

Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.

The Boltzmann distributions of molecular structures predict likely changes through random mutations.

New folded molecular structures can only evolve after arising through mutations. This aspect is modeled using genotype-phenotype maps, which connect sequence changes through mutations to changes in molecular structures. Previous work has shown that the likelihood of appearing through mutations can differ by orders of magnitude from structure to structure and that this can affect the outcomes of evolutionary processes. Thus, we focus on the phenotypic mutation probabilities φqp, i.e., the likelihood that a random mutation changes structure p into structure q. For both RNA secondary structures and the HP protein model, we show that a simple biophysical principle can explain and predict how this likelihood depends on the new structure q: φqp is high if sequences that fold into p as the minimum-free-energy structure are likely to have q as an alternative structure with high Boltzmann frequency. This generalizes the existing concept of plastogenetic congruence from individual sequences to the entire neutral spaces of structures. Our result helps us understand why some structural changes are more likely than others, may be useful for estimating these likelihoods via sampling and makes a connection to alternative structures with high Boltzmann frequency, which could be relevant in evolutionary processes.

The non-deterministic genotype-phenotype map of RNA secondary structure.

Selection and variation are both key aspects in the evolutionary process. Previous research on the mapping between molecular sequence (genotype) and molecular fold (phenotype) has shown the presence of several structural properties in different biological contexts, implying that these might be universal in evolutionary spaces. The deterministic genotype-phenotype (GP) map that links short RNA sequences to minimum free energy secondary structures has been studied extensively because of its computational tractability and biologically realistic nature. However, this mapping ignores the phenotypic plasticity of RNA. We define a GP map that incorporates non-deterministic (ND) phenotypes, and take RNA as a case study; we use the Boltzmann probability distribution of folded structures and examine the structural properties of ND GP maps for RNA sequences of length 12 and coarse-grained RNA structures of length 30 (RNAshapes30). A framework is presented to study robustness, evolvability and neutral spaces in the ND map. This framework is validated by demonstrating close correspondence between the ND quantities and sample averages of their deterministic counterparts. When using the ND framework we observe the same structural properties as in the deterministic GP map, such as bias, negative correlation between genotypic robustness and evolvability, and positive correlation between phenotypic robustness and evolvability.

Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.

The genotype-phenotype (GP) map of RNA secondary structure links each RNA sequence to its corresponding secondary structure. Previous research has shown that the large-scale structural properties of GP maps, such as the size of neutral sets in genotype space, can influence evolutionary outcomes. In order to use neutral set sizes, efficient and accurate computational methods are needed to compute them. Here, we propose a new method, which is based on free energy estimates and is much faster than existing sample-based methods. Moreover, this approach can give insight into the reasons behind neutral set size variations, for example, why structures with fewer stacks tend to have larger neutral set sizes. In addition, we generalize neutral set size calculations from the previously studied many-to-one framework, where each sequence folds into a single energetically preferred structure, to a fuller many-to-many framework, where several low-energy structures are included. We find that structures with high neutral sets in one framework also tend to have large neutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.

Insertions and deletions in the RNA sequence-structure map.

Genotype-phenotype maps link genetic changes to their fitness effect and are thus an essential component of evolutionary models. The map between RNA sequences and their secondary structures is a key example and has applications in functional RNA evolution. For this map, the structural effect of substitutions is well understood, but models usually assume a constant sequence length and do not consider insertions or deletions. Here, we expand the sequence-structure map to include single nucleotide insertions and deletions by using the RNAshapes concept. To quantify the structural effect of insertions and deletions, we generalize existing definitions for robustness and non-neutral mutation probabilities. We find striking similarities between substitutions, deletions and insertions: robustness to substitutions is correlated with robustness to insertions and, for most structures, to deletions. In addition, frequent structural changes after substitutions also tend to be common for insertions and deletions. This is consistent with the connection between energetically suboptimal folds and possible structural transitions. The similarities observed hold both for genotypic and phenotypic robustness and mutation probabilities, i.e. for individual sequences and for averages over sequences with the same structure. Our results could have implications for the rate of neutral and non-neutral evolution.

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics.

Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.

A review of hyperacusis and future directions: part II. Measurement, mechanisms, and treatment.

PURPOSE: Hyperacusis can be extremely debilitating, and at present, there is no cure. In this detailed review of the field, we consolidate present knowledge in the hope of facilitating future research. METHOD: We review and reference the literature on hyperacusis and related areas. This is the 2nd of a 2-part review. RESULTS: Hyperacusis encompasses a wide range of reactions to sounds, which can be grouped into the categories of excessive loudness, annoyance, fear, and pain. Reasonable approaches to assessing the different forms of hyperacusis are emerging, including brain-imaging studies. Researchers are only beginning to understand the many mechanisms at play, and valid animal models are still evolving. There are many counseling and sound-therapy approaches that some patients find helpful, but well-controlled studies are needed to measure their long-term efficacy and to test new approaches. CONCLUSIONS: Hyperacusis can make life difficult in this increasingly noisy world, forcing sufferers to dramatically alter their work and social habits. We believe this is an opportune time to explore approaches to better understand and treat hyperacusis.

A review of hyperacusis and future directions: part I. Definitions and manifestations.

PURPOSE: Hyperacusis can be extremely debilitating, and at present, there is no cure. We provide an overview of the field, and possible related areas, in the hope of facilitating future research. METHOD: We review and reference literature on hyperacusis and related areas. We have divided the review into 2 articles. In Part I, we discuss definitions, epidemiology, different etiologies and subgroups, and how hyperacusis affects people. In Part II, we review measurements, models, mechanisms, and treatments, and we finish with some suggestions for further research. RESULTS: Hyperacusis encompasses a wide range of reactions to sound, which can be grouped into the categories of excessive loudness, annoyance, fear, and pain. Many different causes have been proposed, and it will be important to appreciate and quantify different subgroups. Reasonable approaches to assessing the different forms of hyperacusis are emerging, including psychoacoustical measures, questionnaires, and brain imaging. CONCLUSIONS: Hyperacusis can make life difficult for many, forcing sufferers to dramatically alter their work and social habits. We believe this is an opportune time to explore approaches to better understand and treat hyperacusis.

Kinesin-5 is not essential for mitotic spindle elongation in Dictyostelium.

The proper assembly and operation of the mitotic spindle is essential to ensure the accurate segregation of chromosomes and to position the cytokinetic furrow during cell division in eukaryotes. Not only are dynamic microtubules required but also the concerted actions of multiple motor proteins are necessary to effect spindle pole separation, chromosome alignment, chromatid segregation, and spindle elongation. Although a number of motor proteins are known to play a role in mitosis, there remains a limited understanding of their full range of functions and the details by which they interact with other spindle components. The kinesin-5 (BimC/Eg5) family of motors is largely considered essential to drive spindle pole separation during the initial and latter stages of mitosis. We have deleted the gene encoding the kinesin-5 member in Dictyostelium, (kif13), and find that, in sharp contrast with results found in vertebrate, fly, and yeast organisms, kif13(-) cells continue to grow at rates indistinguishable from wild type. Phenotype analysis reveals a slight increase in spindle elongation rates in the absence of Kif13. More importantly, there is a dramatic, premature separation of spindle halves in kif13(-) cells, suggesting a novel role of this motor in maintaining spindle integrity at the terminal stages of division.

Revised determination of free and complexed myrosinase activities in plant extracts.

The enzyme myrosinase (thioglucoside glucohydrolase, EC 3.2.1.147, formerly EC 3.2.3.1) catalyzes the hydrolysis of glucosinolates after tissue damage in plants of the order Brassicales. The various myrosinase isoforms occur either as free soluble dimers or as insoluble complexes. We propose a reliable method for determination of both soluble and insoluble myrosinase activity concentrations in partially purified plant extracts. The procedure requires the removal of endogenous glucosinolates through ion-exchange columns previous to enzyme measurements. Myrosinase activity was assayed in continuous mode by photometric quantification of the released glucose using glucose-oxidase with peroxidase and colorimetric indicators. The measurement of the colored product at 492nm has a favorable signal to noise ratio both in clear extract solutions (free dimers) and in turbid pellet suspensions (insoluble complexes). No interferences by ascorbic acid were found in continuous analyses. With the recommended sample preparation methods and assay conditions potential activities in damaged plant tissues can be characterized which are involved in plant defense mechanisms.

Specificity of induction responses in Sinapis alba L.: Plant growth and development.

Plant defenses are expected to be negatively correlated with plant growth, development and reproduction. In a recent study, we investigated the specificity of induction responses of chemical defenses in the Brassicaceae Sinapis alba.1 It was shown that glucosinolate levels and myrosinase activities increased to different degrees after 24-hours-feeding by a specialist or generalist herbivore or mechanical wounding. Here, we present the specific influences of these treatments on organ biomasses which were recorded as a measure of growth. Directly after the treatments, organ biomasses were reduced locally and systemically by herbivore feeding, but not by mechanical wounding compared to control plants. Induction of glucosinolates, which increased in all treatments, is thus not necessarily expressed as cost in terms of reduced growth in S. alba. No significant long-term differences in plant development between herbivore treated and control plants were found. Thus, tissue loss and increased investments in chemical defenses could be compensated over time, but compensation patterns depended on the inducing agent. Furthermore, herbivore treatments resulted in an increased mechanical defense, measured as abaxial trichome densities. Plants respond highly dynamic with regard to defense and growth allocation and due to different inductors.

Specificity of induction responses in Sinapis alba L. and their effects on a specialist herbivore.

The glucosinolate-myrosinase system of Brassicaceae is known to hold a defensive function in both a constitutive and an inducible fashion. Glucosinolates are sulfur- and nitrogen-containing metabolites that are hydrolyzed upon tissue disruption by myrosinase enzymes. The resulting products are toxic for most herbivores. Nevertheless, some insects evolved detoxification mechanisms that enable them to feed exclusively on Brassicaceae. Induction of plant chemical defenses that deter or poison generalists might be ineffective against adapted specialists. We investigated the specificity of short-term induction patterns of chemical defenses in Sinapis alba damaged by a glucosinolate-sequestering specialist herbivore (turnip sawfly, Athalia rosae), a generalist herbivore (fall armyworm, Spodoptera frugiperda), or mechanical wounding (cork borer), and their effects on the behavior of A. rosae. After 24 hr of damage to young leaves, local as well as systemic changes in glucosinolate and myrosinase levels were analyzed. The intensity of the resulting changes was highest in damaged leaves. Induction responses in S. alba were dependent upon the attacking herbivore and were distinct from a mere wound response. Specialist feeding and mechanical wounding evoked up to threefold increases in levels of both parts of the glucosinolate-myrosinase system, whereas generalist feeding induced up to twofold increases in glucosinolate levels only. The majority of constitutive and induced myrosinase activity was found in the insoluble fractions. Possible consequences for the plant-specialist interaction were examined in behavioral tests with larvae and adult females of A. rosae on induced S. alba plants. Larval feeding and adult oviposition patterns were not modulated in relation to plant treatment. Thus, specificity was found in S. alba responses in relation to the inducing agent, but it was not present in return in the effects on the behavior of an adapted herbivore.