Competitive exclusion and coexistence of universal grammars

Universal grammar (UG) is a list of innate constraints that specify the set of grammars that can be learned by the child during primary language acquisition. UG of the human brain has been shaped by evolution. Evolution requires variation. Hence, we have to postulate and study variation of UG. We investigate evolutionary dynamics and language acquisition in the context of multiple UGs. We provide examples for competitive exclusion and stable coexistence of different UGs. More specific UGs admit fewer candidate grammars, and less specific UGs admit more candidate grammars. We will analyze conditions for more specific UGs to outcompete less specific UGs and vice versa. An interesting finding is that less specific UGs can resist invasion by more specific UGs if learning is more accurate. In other words, accurate learning stabilizes UGs that admit large numbers of candidate grammars.     

Language dynamics in finite populations

Any mechanism of language acquisition can only learn a restricted set of grammars. The human brain contains a mechanism for language acquisition which can learn a restricted set of grammars. The theory of this restricted set is universal grammar (UG). UG has to be sufficiently specific to induce linguistic coherence in a population. This phenomenon is known as "coherence threshold". Previously, we have calculated the coherence threshold for deterministic dynamics and infinitely large populations. Here, we extend the framework to stochastic processes and finite populations. If there is selection for communicative function (selective language dynamics), then the analytic results for infinite populations are excellent approximations for finite populations; as expected, finite populations need a slightly higher accuracy of language acquisition to maintain coherence. If there is no selection for communicative function (neutral language dynamics), then linguistic coherence is only possible for finite populations.     

The genetic code constrains yet facilitates Darwinian evolution

An important goal of evolutionary biology is to understand the constraints that shape the dynamics and outcomes of evolution. Here, we address the extent to which the structure of the standard genetic code constrains evolution by analyzing adaptive mutations of the antibiotic resistance gene TEM-1 β-lactamase and the fitness distribution of codon substitutions in two influenza hemagglutinin inhibitor genes. We find that the architecture of the genetic code significantly constrains the adaptive exploration of sequence space. However, the constraints endow the code with two advantages: the ability to restrict access to amino acid mutations with a strong negative effect and, most remarkably, the ability to enrich for adaptive mutations. Our findings support the hypothesis that the standard genetic code was shaped by selective pressure to minimize the deleterious effects of mutation yet facilitate the evolution of proteins through imposing an adaptive mutation bias.     

The structure of mutations and the evolution of cooperation

Evolutionary game dynamics in finite populations assumes that all mutations are equally likely, i.e., if there are n strategies a single mutation can result in any strategy with probability 1/n. However, in biological systems it seems natural that not all mutations can arise from a given state. Certain mutations may be far away, or even be unreachable given the current composition of an evolving population. These distances between strategies (or genotypes) define a topology of mutations that so far has been neglected in evolutionary game theory. In this paper we re-evaluate classic results in the evolution of cooperation departing from the assumption of uniform mutations. We examine two cases: the evolution of reciprocal strategies in a repeated prisoner's dilemma, and the evolution of altruistic punishment in a public goods game. In both cases, alternative but reasonable mutation kernels shift known results in the direction of less cooperation. We therefore show that assuming uniform mutations has a substantial impact on the fate of an evolving population. Our results call for a reassessment of the "model-less" approach to mutations in evolutionary dynamics.     

A mouse model for poliovirus neurovirulence identifies mutations that attenuate the virus for humans.

A mutation in the genome of poliovirus type 3 that is known to reduce neurovirulence in humans similarly reduces neurovirulence in mice when incorporated into a mouse-adapted-human poliovirus recombinant. Viral recombinants with a uracil at nucleotide position 472 in the 5'-noncoding regions of their genomes are unable to replicate in the mouse brain. Viral recombinants with a cytosine at this position are neurovirulent in mice. Neurovirulence of poliovirus in mice may therefore prove to be a useful indicator of the genetic stability of new attenuating mutations created by site-directed mutagenesis.     

Artificial Grammar Learning of Melody Is Constrained by Melodic Inconsistency: Narmour's Principles Affect Melodic Learning

Considerable evidence suggests that people acquire artificial grammars incidentally and implicitly, an indispensable capacity for the acquisition of music or language. However, less research has been devoted to exploring constraints affecting incidental learning. Within the domain of music, the extent to which Narmour''s (1990) melodic principles affect implicit learning of melodic structure was experimentally explored. Extending previous research (Rohrmeier, Rebuschat & Cross, 2011), the identical finite-state grammar is employed having terminals (the alphabet) manipulated so that melodies generated systematically violated Narmour''s principles. Results indicate that Narmour-inconsistent melodic materials impede implicit learning. This further constitutes a case in which artificial grammar learning is affected by prior knowledge or processing constraints.     

Revisiting the syntactic abilities of non-human animals: natural vocalizations and artificial grammar learning

The domain of syntax is seen as the core of the language faculty and as the most critical difference between animal vocalizations and language. We review evidence from spontaneously produced vocalizations as well as from perceptual experiments using artificial grammars to analyse animal syntactic abilities, i.e. abilities to produce and perceive patterns following abstract rules. Animal vocalizations consist of vocal units (elements) that are combined in a species-specific way to create higher order strings that in turn can be produced in different patterns. While these patterns differ between species, they have in common that they are no more complex than a probabilistic finite-state grammar. Experiments on the perception of artificial grammars confirm that animals can generalize and categorize vocal strings based on phonetic features. They also demonstrate that animals can learn about the co-occurrence of elements or learn simple 'rules' like attending to reduplications of units. However, these experiments do not provide strong evidence for an ability to detect abstract rules or rules beyond finite-state grammars. Nevertheless, considering the rather limited number of experiments and the difficulty to design experiments that unequivocally demonstrate more complex rule learning, the question of what animals are able to do remains open.     

Genetic versus phenotypic models of selection: can genetics be neglected in a long-term perspective?

Game theoretical concepts in evolutionary biology have been criticized by populations geneticists, because they neglect such crucial aspects as the mating system or the mode of inheritance. In fact, the dynamics of natural selection does not necessarily lead to a fitness maximum or an ESS if genetic constraints are taken into account. Yet, it may be premature to conclude that game theoretical concepts do not have a dynamical justification. The new paradigm of long-term evolution postulates that genetic constraints, which may be dominant in a short-term perspective, will in the long run disappera in the face of the ongoing influx of mutations. Two basic results (see Hammerstein; this issue) seem to reconcile the dynamical approach of long-term population genetics with the static approach of evolutionary game theory: (1) only populations at local fitness optima (Nash strategies) can be long-term stable; and (2) in monomorphic populations, evolutionary stability is necessary and sufficient to ensure long-term dynamic stability. The present paper has a double purpose. On the one hand, it is demonstrated by fairly general arguments that the scope of the results mentioned above extends to non-linear frequency dependent selection, to multiple loci, and to quite general mating systems. On the other hand, some limitations of the theory of long-term evolution will also be stressed: (1) there is little hope for a game theoretical characterization of stability in polymorphic populations; (2) many interesting systems do not admit long-term stable equilibria; and (3) even if a long-term stable equilibrium exists, it is not at all clear whether and how it is attainable by a series of gene substition events.     

Fluctuating Asymmetry of Responders Affects Offers in the Ultimatum Game Oppositely According to Attractiveness or Need as Perceived by Proposers

The Ultimatum Game (UG) measures cooperative tendencies in humans. A proposer offers to split a given sum of money between self and a responder, who may accept or reject the offer. If accepted, each receives the proposed split; if rejected, nobody receives anything. We studied the effect of the putative responder's degree of facial symmetry (fluctuating asymmetry, FA) on the offer he/she received in opposite-sexed UGs. Symmetry is an important measure of biological quality so subjects were expected to receive higher offers when symmetrical than asymmetrical. In a sample of Jamaicans, individuals played two UGs with opposite-sexed responders, a symmetrical photo of a Lebanese and an asymmetrical one. Individuals do indeed give more to symmetrical responders (p = 0.032). When subjects are asked their motivation, a striking dichotomy emerges: those who cite 'attractiveness' as a motive, give strongly to symmetrical responders while those citing 'need' invariably give more to asymmetrical ones (p < 0.0001). Females also show a nearly significant tendency to cite need as a motive more often than do males.     

LIFE AT THE FRONT OF AN EXPANDING POPULATION

Environmental changes have caused episodes of habitat expansions in the evolutionary history of many species. These range changes affect the dynamics of biological evolution in multiple ways. Recent microbial experiments as well as simulations suggest that enhanced genetic drift at the frontier of a two-dimensional range expansion can cause genetic sectoring patterns with fractal domain boundaries. Here, we propose and analyze a simple model of asexual biological evolution at expanding frontiers that explains these neutral patterns and predicts the effect of natural selection. We find that beneficial mutations give rise to sectors with an opening angle that depends sensitively on the selective advantage of the mutants. Deleterious mutations, on the other hand, are not able to establish a sector permanently. They can, however, temporarily "surf" on the population front, and thereby reach unusually high frequencies. As a consequence, expanding frontiers are loaded with a high fraction of mutants at mutation–selection balance. Numerically, we also determine the condition at which the wild type is lost in favor of deleterious mutants (genetic meltdown) at a growing front. Our prediction for this error threshold differs qualitatively from existing well-mixed theories, and sets tight constraints on sustainable mutation rates for populations that undergo frequent range expansions.     

Global mutations and local mutations have very different effects on evolution, illustrated by mixed strategies of asymmetric binary games

We study the evolutionary effect of rare mutations causing global changes in traits. We consider asymmetric binary games between two players. The first player takes two alternative options with probability x and 1−x; and the second player takes options with probability y and 1−y. Due to natural selection and recurrent mutation, the population evolves to have broad distributions of x and y. We analyze three cases showing qualitatively different dynamics, exemplified by (1) vigilance-intrusion game, (2) asymmetric hawk-dove game and (3) cleaner-client game. We found that the evolutionary outcome is strongly dependent upon the distribution of mutants’ traits, more than the mutation rates. For example in the vigilance-intrusion game, the evolutionary dynamics show a perpetual stable oscillation if mutants are always close to the parent (local-mutation mode), whilst the population converges to a stable equilibrium distribution if mutants can be quite different from the parent (global-mutation mode), even for extremely low mutation rate. When common local mutations and rare global mutations occur simultaneously, the evolutionary outcome is controlled by the latter.     

The neurobiology of syntax: beyond string sets

The human capacity to acquire language is an outstanding scientific challenge to understand. Somehow our language capacities arise from the way the human brain processes, develops and learns in interaction with its environment. To set the stage, we begin with a summary of what is known about the neural organization of language and what our artificial grammar learning (AGL) studies have revealed. We then review the Chomsky hierarchy in the context of the theory of computation and formal learning theory. Finally, we outline a neurobiological model of language acquisition and processing based on an adaptive, recurrent, spiking network architecture. This architecture implements an asynchronous, event-driven, parallel system for recursive processing. We conclude that the brain represents grammars (or more precisely, the parser/generator) in its connectivity, and its ability for syntax is based on neurobiological infrastructure for structured sequence processing. The acquisition of this ability is accounted for in an adaptive dynamical systems framework. Artificial language learning (ALL) paradigms might be used to study the acquisition process within such a framework, as well as the processing properties of the underlying neurobiological infrastructure. However, it is necessary to combine and constrain the interpretation of ALL results by theoretical models and empirical studies on natural language processing. Given that the faculty of language is captured by classical computational models to a significant extent, and that these can be embedded in dynamic network architectures, there is hope that significant progress can be made in understanding the neurobiology of the language faculty.     

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.     

A Ruby in the Rubbish: Beneficial Mutations, Deleterious Mutations and the Evolution of Sex

This study presents a mathematical model in which a single beneficial mutation arises in a very large population that is subject to frequent deleterious mutations. The results suggest that, if the population is sexual, then the deleterious mutations will have little effect on the ultimate fate of the beneficial mutation. However, if most offspring are produced asexually, then the probability that the beneficial mutation will be lost from the population may be greatly enhanced by the deleterious mutations. Thus, sexual populations may adapt much more quickly than populations where most reproduction is asexual. Some of the results were produced using computer simulation methods, and a technique was developed that allows treatment of arbitrarily large numbers of individuals in a reasonable amount of computer time. This technique may be of prove useful for the analysis of a wide variety of models, though there are some constraints on its applicability. For example, the technique requires that reproduction can be described by Poisson processes.     

Mutation in evolutionary games can increase average fitness at equilibrium

We study game dynamical interactions between two strategies, A and B, and analyse whether the average fitness of the population at equilibrium can be increased by adding mutation from A to B. Classifying all two by two games with payoff matrix [(a,b),(c,d)], we show that mutation from A to B enhances the average fitness of the whole population (i) if both a and d are less than (b + c)/2 and (ii) if c is less than b. Furthermore, we study conditions for maximizing the productivity of strategy A, and we analyse the effect of mutations in both directions. Depending on the biological system, a mutation in an evolutionary game can be interpreted as a genetic alteration, a cellular differentiation, a change in gene expression, an accidental or deliberate modification in cultural transmission, or a learning error. In a cultural context, our results indicate that the equilibrium payoff of the population can be increased if players sometimes choose the strategy with lower payoff. In a genetic context, we have shown that for frequency-dependent selection mutation can enhance the average fitness of the population at equilibrium.     

A stochastic context free grammar based framework for analysis of protein sequences

Background  

In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited the application of formal language theory to the production of grammars whose expressive power is not higher than stochastic regular grammars. However, these grammars, like other state of the art methods, cannot cover any higher-order dependencies such as nested and crossing relationships that are common in proteins. In order to overcome some of these limitations, we propose a Stochastic Context Free Grammar based framework for the analysis of protein sequences where grammars are induced using a genetic algorithm.     

Apparent directional selection by biased pleiotropic mutation

Pleiotropic effects of deleterious mutations are considered to be among the factors responsible for genetic constraints on evolution by long-term directional selection acting on a quantitative trait. If pleiotropic phenotypic effects are biased in a particular direction, mutations generate apparent directional selection, which refers to the covariance between fitness and the trait owing to a linear association between the number of mutations possessed by individuals and the genotypic values of the trait. The present analysis has shown how the equilibrium mean value of the trait is determined by a balance between directional selection and biased pleiotropic mutations. Assuming that genes act additively both on the trait and on fitness, the total variance-standardized directional selection gradient was decomposed into apparent and true components. Experimental data on mutation bias from the bristle traits of Drosophila and life history traits of Daphnia suggest that apparent selection explains a small but significant fraction of directional selection pressure that is observed in nature; the data suggest that changes induced in a trait by biased pleiotropic mutation (i.e., by apparent directional selection) are easily compensated for by (true) directional selection.     

Phenylketonuria and the peoples of Northern Ireland

The comparison of regional patterns of recessive disease mutations is a new source of information for studies of population genetics. The analysis of phenylketonuria (PKU) mutations in Northern Ireland shows that most major episodes of immigration have left a record in the modern genepool. The mutation I65T can be traced to the Palaeolithic people of western Europe who, in the Mesolithic period, first colonised Ireland. R408W (on haplotype 1) in contrast, the most common Irish PKU mutation, may have been prevalent in the Neolithic farmers who settled in Ireland after 4500 BC. No mutation was identified that could represent European Celtic populations, supporting the view that the adoption of Celtic culture and language in Ireland did not involve major migration from the continent. Several less common mutations can be traced to the Norwegian Atlantic coast and were probably introduced into Ireland by Vikings. This indicates that PKU has not been brought to Norway from the British Isles, as was previously argued. The rarity in Northern Ireland of IVS12nt1, the most common mutation in Denmark and England, indicates that the English colonialisation of Ireland did not alter the local genepool in a direction that could be described as Anglo-Saxon. Our results show that the culture and language of a population can be independent of its genetic heritage, and give some insight into the history of the peoples of Northern Ireland. Received: 23 October 1996 / Accepted: 26 February 1997