Dynamics of transcription factor binding site evolution

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ~10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of "pre-sites" or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genetics.Comment: 28 pages, 15 figure

Culture Outsmarts Nature in the Evolution of Cooperation

A one dimensional cellular automata model describes the evolutionary dynamics of cooperation when grouping by cooperators provides protection against predation. It is used to compare the dynamics of evolution of cooperation in three settings. G: only vertical transmission of information is allowed, as an analogy of genetic evolution with heredity; H: only horizontal information transfer is simulated, through diffusion of the majority\'s opinion, as an analogy of opinion dynamics or social learning; and C: analogy of cultural evolution, where information is transmitted both horizontally (H) and vertically (V) so that learned behavior can be transmitted to offspring. The results show that the prevalence of cooperative behavior depends on the costs and benefits of cooperation so that: a- cooperation becomes the dominant behavior, even in the presence of free-riders (i.e., non-cooperative obtaining benefits from the cooperation of others), under all scenarios, if the benefits of cooperation compensate for its cost; b- G is more susceptible to selection pressure than H achieving a closer adaptation to the fitness landscape; c- evolution of cooperative behavior in H is less sensitive to the cost of cooperation than in G; d- C achieves higher levels of cooperation than the other alternatives at low costs, whereas H does it at high costs. The results suggest that a synergy between H and V is elicited that makes the evolution of cooperation much more likely under cultural evolution than under the hereditary kind where only V is present.Social Simulation, Interactions, Group Size, Selfish Heard, Cultural Evolution, Biological Evolution

Extended Inclusive Fitness Theory bridges Economics and Biology through a common understanding of Social Synergy

Inclusive Fitness Theory (IFT) was proposed half a century ago by W.D. Hamilton to explain the emergence and maintenance of cooperation between individuals that allows the existence of society. Contemporary evolutionary ecology identified several factors that increase inclusive fitness, in addition to kin-selection, such as assortation or homophily, and social synergies triggered by cooperation. Here we propose an Extend Inclusive Fitness Theory (EIFT) that includes in the fitness calculation all direct and indirect benefits an agent obtains by its own actions, and through interactions with kin and with genetically unrelated individuals. This formulation focuses on the sustainable cost/benefit threshold ratio of cooperation and on the probability of agents sharing mutually compatible memes or genes. This broader description of the nature of social dynamics allows to compare the evolution of cooperation among kin and non-kin, intra- and inter-specific cooperation, co-evolution, the emergence of symbioses, of social synergies, and the emergence of division of labor. EIFT promotes interdisciplinary cross fertilization of ideas by allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics.Comment: Bioeconomics, Synergy, Complexit

Landscape and flux for quantifying global stability and dynamics of game theory

Game theory has been widely applied to many areas including economics, biology and social sciences. However, it is still challenging to quantify the global stability and global dynamics of the game theory. We developed a landscape and flux framework to quantify the global stability and global dynamics of the game theory. As an example, we investigated the models of three-strategy games: a special replicator-mutator game, the repeated prison dilemma model. In this model, one stable state, two stable states and limit cycle can emerge under different parameters. The repeated Prisoner's Dilemma system has Hopf bifurcation transitions from one stable state to limit cycle state, and then to another one stable state or two stable states, or vice versa. We explored the global stability of the repeated Prisoner's Dilemma system and the kinetic paths between the basins of attractor. The paths are irreversible due to the non-zero flux. One can explain the game for $Peace$ and $War$.Comment: 25 pages, 15 figure

Vengefulness Evolves in Small Groups

We discuss how small group interactions overcome evolutionary problems that might otherwise erode vengefulness as a preference trait. The basic viability problem is that the fitness benefits of vengeance often do not cover its personal cost. Even when a sufficiently high level of vengefulness brings increased fitness, at lower levels, vengefulness has a negative fitness gradient. This leads to the threshold problem: how can vengefulness become established in the first place? If it somehow becomes established at a high level, vengefulness creates an attractive niche for cheap imitators, those who look like highly vengeful types but do not bear the costs. This is the mimicry problem, and unchecked it could eliminate vengeful traits. We show how within-group social norms can solve these problems even when encounters with outsiders are also important.

Evolutionary consequences of behavioral diversity

Iterated games provide a framework to describe social interactions among groups of individuals. Recent work stimulated by the discovery of "zero-determinant" strategies has rapidly expanded our ability to analyze such interactions. This body of work has primarily focused on games in which players face a simple binary choice, to "cooperate" or "defect". Real individuals, however, often exhibit behavioral diversity, varying their input to a social interaction both qualitatively and quantitatively. Here we explore how access to a greater diversity of behavioral choices impacts the evolution of social dynamics in finite populations. We show that, in public goods games, some two-choice strategies can nonetheless resist invasion by all possible multi-choice invaders, even while engaging in relatively little punishment. We also show that access to greater behavioral choice results in more "rugged " fitness landscapes, with populations able to stabilize cooperation at multiple levels of investment, such that choice facilitates cooperation when returns on investments are low, but hinders cooperation when returns on investments are high. Finally, we analyze iterated rock-paper-scissors games, whose non-transitive payoff structure means unilateral control is difficult and zero-determinant strategies do not exist in general. Despite this, we find that a large portion of multi-choice strategies can invade and resist invasion by strategies that lack behavioral diversity -- so that even well-mixed populations will tend to evolve behavioral diversity.Comment: 26 pages, 4 figure

Evolution of oil droplets in a chemorobotic platform

Evolution, once the preserve of biology, has been widely emulated in software, while physically embodied systems that can evolve have been limited to electronic and robotic devices and have never been artificially implemented in populations of physically interacting chemical entities. Herein we present a liquid-handling robot built with the aim of investigating the properties of oil droplets as a function of composition via an automated evolutionary process. The robot makes the droplets by mixing four different compounds in different ratios and placing them in a Petri dish after which they are recorded using a camera and the behaviour of the droplets analysed using image recognition software to give a fitness value. In separate experiments, the fitness function discriminates based on movement, division and vibration over 21 cycles, giving successive fitness increases. Analysis and theoretical modelling of the data yields fitness landscapes analogous to the genotype–phenotype correlations found in biological evolution. , Trevor Hinkley, James Ward Taylor Kliment Yane

Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions

Eco-evolutionary dynamics on deformable fitness landscapes

Conventional approaches to modelling ecological dynamics often do not include evolutionary changes in the genetic makeup of component species and, conversely, conventional approaches to modelling evolutionary changes in the genetic makeup of a population often do not include ecological dynamics. But recently there has been considerable interest in understanding the interaction of evolutionary and ecological dynamics as coupled processes. However, in the context of complex multi-species ecosytems, especially where ecological and evolutionary timescales are similar, it is difficult to identify general organising principles that help us understand the structure and behaviour of complex ecosystems. Here we introduce a simple abstraction of coevolutionary interactions in a multi-species ecosystem. We model non-trophic ecological interactions based on a continuous but low-dimensional trait/niche space, where the location of each species in trait space affects the overlap of its resource utilisation with that of other species. The local depletion of available resources creates, in effect, a deformable fitness landscape that governs how the evolution of one species affects the selective pressures on other species. This enables us to study the coevolution of ecological interactions in an intuitive and easily visualisable manner. We observe that this model can exhibit either of the two behavioural modes discussed in the literature; namely, evolutionary stasis or Red Queen dynamics, i.e., continued evolutionary change. We find that which of these modes is observed depends on the lag or latency between the movement of a species in trait space and its effect on available resources. Specifically, if ecological change is nearly instantaneous compared to evolutionary change, stasis results; but conversely, if evolutionary timescales are closer to ecological timescales, such that resource depletion is not instantaneous on evolutionary timescales, then Red Queen dynamics result. We also observe that in the stasis mode, the overall utilisation of resources by the ecosystem is relatively efficient, with diverse species utilising different niches, whereas in the Red Queen mode the organisation of the ecosystem is such that species tend to clump together competing for overlapping resources. These models thereby suggest some basic conditions that influence the organisation of inter-species interactions and the balance of individual and collective adaptation in ecosystems, and likewise they also suggest factors that might be useful in engineering artificial coevolution