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## ‣ Evolutionary game theory: Temporal and spatial effects beyond replicator dynamics

Roca, Carlos P.; Cuesta, José A.; Sánchez, Angel
Tipo: info:eu-repo/semantics/acceptedVersion; info:eu-repo/semantics/article Formato: application/pdf
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Evolutionary game dynamics is one of the most fruitful frameworks for studying evolution in different disciplines, from Biology to Economics. Within this context, the approach of choice for many researchers is the so-called replicator equation, that describes mathematically the idea that those individuals performing better have more offspring and thus their frequency in the population grows. While very many interesting results have been obtained with this equation in the three decades elapsed since it was first proposed, it is important to realize the limits of its applicability. One particularly relevant issue in this respect is that of non-meanfield effects, that may arise from temporal fluctuations or from spatial correlations, both neglected in the replicator equation. This review discusses these temporal and spatial effects focusing on the non-trivial modifications they induce when compared to the outcome of replicator dynamics. Alongside this question, the hypothesis of linearity and its relation to the choice of the rule for strategy update is also analyzed. The discussion is presented in terms of the emergence of cooperation, as one of the current key problems in Biology and in other disciplines.; This work has been supported by projects MOSAICO...

## ‣ Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes

Schirtzinger, Erin E.; Tavares, Erika S.; Gonzales, Lauren A.; Eberhard, Jessica R.; Miyaki, Cristina Y.; Sanchez, Juan J.; Hernandez, Alexis; Mueeller, Heinrich; Graves, Gary R.; Fleischer, Robert C.; Wright, Timothy F.
Tipo: Artigo de Revista Científica
Português
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mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Ayes). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes...

## ‣ Imitation Dynamics of Vaccination Behaviour on Social Networks

Nowak, Martin A.; Fu, Feng; Rosenbloom, Daniel I; Wang, Longfei
Fonte: Royal Society of London Publicador: Royal Society of London
Tipo: Artigo de Revista Científica
Português
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The problem of achieving widespread immunity to infectious diseases by voluntary vaccination is often presented as a public-goods dilemma, as an individual's vaccination contributes to herd immunity, protecting those who forgo vaccination. The temptation to free-ride brings the equilibrium vaccination level below the social optimum. Here, we present an evolutionary game-theoretic approach to this problem, exploring the roles of individual imitation behaviour and population structure in vaccination. To this end, we integrate an epidemiological process into a simple agent-based model of adaptive learning, where individuals use anecdotal evidence to estimate costs and benefits of vaccination. In our simulations, we focus on parameter values that are realistic for a flu-like infection. Paradoxically, as agents become more adept at imitating successful strategies, the equilibrium level of vaccination falls below the rational individual optimum. In structured populations, the picture is only somewhat more optimistic: vaccination is widespread over a range of low vaccination costs, but coverage plummets after cost exceeds a critical threshold. This result suggests parallels to historical scenarios in which vaccination coverage provided herd immunity for some time...

## ‣ Distilling the Essence of an Evolutionary Process and Implications for a Formal Description of Culture

Gabora, Liane; Aerts, Diederik
Tipo: Artigo de Revista Científica
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It has been proposed that, since the origin of life and the ensuing evolution of biological species, a second evolutionary process has appeared on our planet. It is the evolution of culture-e.g., ideas, beliefs, and artifacts. Does culture evolve in the same genuine sense as biological life? And if so, does it evolve through natural selection, or by some other means? Why does no other species remotely approach the degree of cultural complexity of humans? These questions lie at the foundation of who we are and what makes our lives meaningful. Although much research has been done on how selective pressures operating at the biological level affect cognition and culture, little research has focused on culture as an evolutionary process in its own right. Like biological forms, cultural forms-ideas, attitudes, artifacts, mannerisms, etc.-incrementally adapt to the constraints and affordances of their environment through descent with modification. In some respects culture appears to be Darwinian, i.e., a process of differential replication and selection amongst randomly generated variants. This suggests that knowledge of biological evolution can be put to use to gain insight into culture. However, attempts to apply Darwinian theory to culture have not yielded the kind of unifying framework for the social sciences that it provided for the biological sciences...

## ‣ A Computational Method for the Rate Estimation of Evolutionary Transpositions

Alexeev, Nikita; Aidagulov, Rustem; Alekseyev, Max A.
Tipo: Artigo de Revista Científica
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Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as transpositions, they are rarely observed and believed to constitute only a small fraction of genome rearrangements happening in the course of evolution. The analysis of transpositions is further obfuscated by intractability of the underlying computational problems. We propose a computational method for estimating the rate of transpositions in evolutionary scenarios between genomes. We applied our method to a set of mammalian genomes and estimated the transpositions rate in mammalian evolution to be around 0.26.; Comment: Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), 2015. (to appear)

## ‣ Scaling properties of protein family phylogenies

Herrada, E. Alejandro; Eguíluz, Víctor M.; Hernández-García, Emilio; Duarte, Carlos M.
Tipo: Artigo de Revista Científica
Português
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One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of balance) of a large set of protein phylogenies with a set of species phylogenies. The comparative analysis shows that both sets of phylogenies share remarkably similar scaling behavior, suggesting the universality of branching rules and of the evolutionary processes that drive biological diversification from gene to species level. In order to explain such generality, we propose a simple model which allows us to estimate the proportion of evolvability/robustness needed to approximate the scaling behavior observed in the phylogenies, highlighting the relevance of the robustness of a biological system (species or protein) in the scaling properties of the phylogenetic trees. Thus, the rules that govern the incapability of a biological system to diversify are equally relevant both at the gene and at the species level.; Comment: Replaced with final published version

## ‣ Small games and long memories promote cooperation

Stewart, Alexander J.; Plotkin, Joshua B.
Tipo: Artigo de Revista Científica
Português
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Complex social behaviors lie at the heart of many of the challenges facing evolutionary biology, sociology, economics, and beyond. For evolutionary biologists in particular the question is often how such behaviors can arise \textit{de novo} in a simple evolving system. How can group behaviors such as collective action, or decision making that accounts for memories of past experience, emerge and persist? Evolutionary game theory provides a framework for formalizing these questions and admitting them to rigorous study. Here we develop such a framework to study the evolution of sustained collective action in multi-player public-goods games, in which players have arbitrarily long memories of prior rounds of play and can react to their experience in an arbitrary way. To study this problem we construct a coordinate system for memory-$m$ strategies in iterated $n$-player games that permits us to characterize all the cooperative strategies that resist invasion by any mutant strategy, and thus stabilize cooperative behavior. We show that while larger games inevitably make cooperation harder to evolve, there nevertheless always exists a positive volume of strategies that stabilize cooperation provided the population size is large enough. We also show that...

## ‣ Clustering genes of common evolutionary history

Gori, Kevin; Suchan, Tomasz; Alvarez, Nadir; Goldman, Nick; Dessimoz, Christophe
Tipo: Artigo de Revista Científica
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Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modelling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion...

## ‣ Universal power law behaviors in genomic sequences and evolutionary models

Martignetti, L.; Caselle, M.
Tipo: Artigo de Revista Científica
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We study the length distribution of a particular class of DNA sequences known as 5'UTR exons. These exons belong to the messanger RNA of protein coding genes, but they are not coding (they are located upstream of the coding portion of the mRNA) and are thus less constrained from an evolutionary point of view. We show that both in mouse and in human these exons show a very clean power law decay in their length distribution and suggest a simple evolutionary model which may explain this finding. We conjecture that this power law behaviour could indeed be a general feature of higher eukaryotes.; Comment: 15 pages, 3 figures

## ‣ Large Fluctuations and Fixation in Evolutionary Games

Assaf, Michael; Mobilia, Mauro
Tipo: Artigo de Revista Científica
Português
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We study large fluctuations in evolutionary games belonging to the coordination and anti-coordination classes. The dynamics of these games, modeling cooperation dilemmas, is characterized by a coexistence fixed point separating two absorbing states. We are particularly interested in the problem of fixation that refers to the possibility that a few mutants take over the entire population. Here, the fixation phenomenon is induced by large fluctuations and is investigated by a semi-classical WKB (Wentzel-Kramers-Brillouin) theory generalized to treat stochastic systems possessing multiple absorbing states. Importantly, this method allows us to analyze the combined influence of selection and random fluctuations on the evolutionary dynamics \textit{beyond} the weak selection limit often considered in previous works. We accurately compute, including pre-exponential factors, the probability distribution function in the long-lived coexistence state and the mean fixation time necessary for a few mutants to take over the entire population in anti-coordination games, and also the fixation probability in the coordination class. Our analytical results compare excellently with extensive numerical simulations. Furthermore, we demonstrate that our treatment is superior to the Fokker-Planck approximation when the selection intensity is finite.; Comment: 17 pages...

## ‣ Predicting protein contact map using evolutionary and physical constraints by integer programming (extended version)

Wang, Zhiyong; Xu, Jinbo
Tipo: Artigo de Revista Científica
Português
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Motivation. Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains very challenging to predict contact map using only sequence information. Most existing methods predict the contact map matrix element-by-element, ignoring correlation among contacts and physical feasibility of the whole contact map. A couple of recent methods predict contact map based upon residue co-evolution, taking into consideration contact correlation and enforcing a sparsity restraint, but these methods require a very large number of sequence homologs for the protein under consideration and the resultant contact map may be still physically unfavorable. Results. This paper presents a novel method PhyCMAP for contact map prediction, integrating both evolutionary and physical restraints by machine learning and integer linear programming (ILP). The evolutionary restraints include sequence profile, residue co-evolution and context-specific statistical potential. The physical restraints specify more concrete relationship among contacts than the sparsity restraint. As such, our method greatly reduces the solution space of the contact map matrix and thus...

## ‣ Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game

Basanta, David; Scott, Jacob G; Fishman, Mayer N; Ayala, Gustavo E; Hayward, Simon W; Anderson, Alexander RA
Tipo: Artigo de Revista Científica
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Tumours are made up of a mixed population of different types of cells that include normal struc- tures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a math- ematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the cancer; (ii) early in its genesis the tumour acquires a highly malignant phenotype, growing rapidly and displacing the original stromal population (often referred to as small cell prostate cancer) - these less common aggressive tumours are relatively independent of the local microenvironment; and, (iii) the tumour co-opts the local stroma - taking on a classic stromagenic phenotype where interactions with the local microenviron- ment are critical to the cancer growth. We present an evolutionary game theoretical construct that models the influence of tumour-stroma interactions in driving these outcomes. We consider three characteristic and distinct cellular populations: stromal cells...

## ‣ Rewarding evolutionary fitness with links between populations promotes cooperation

Wang, Zhen; Szolnoki, Attila; Perc, Matjaz
Tipo: Artigo de Revista Científica
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Evolution of cooperation in the prisoner's dilemma and the public goods game is studied, where initially players belong to two independent structured populations. Simultaneously with the strategy evolution, players whose current utility exceeds a threshold are rewarded by an external link to a player belonging to the other population. Yet as soon as the utility drops below the threshold, the external link is terminated. The rewarding of current evolutionary fitness thus introduces a time-varying interdependence between the two populations. We show that, regardless of the details of the evolutionary game and the interaction structure, the self-organization of fitness and reward gives rise to distinguished players that act as strong catalysts of cooperative behavior. However, there also exist critical utility thresholds beyond which distinguished players are no longer able to percolate. The interdependence between the two populations then vanishes, and cooperators are forced to rely on traditional network reciprocity alone. We thus demonstrate that a simple strategy-independent form of rewarding may significantly expand the scope of cooperation on structured populations. The formation of links outside the immediate community seems particularly applicable in human societies...

## ‣ Chimeric protein complexes in hybrid species generate novel evolutionary phenotypes

Piatkowska, Elzbieta M.; Knight, David; Delneri, Daniela
Tipo: Artigo de Revista Científica
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Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently deemed to be responsible for the phenotypic properties seen in hybrids. However, since the majority of the biological functions in a cell are carried out by protein complexes, inter-specific protein assemblies therefore represent another important source of natural variation upon which evolutionary forces can act. Here we studied the composition of six protein complexes in two different Saccharomyces "sensu strictu" hybrids, to understand whether chimeric interactions can be freely formed in the cell in spite of species-specific co-evolutionary forces, and whether the different types of complexes cause a change in hybrid fitness. The protein assemblies were isolated from the hybrids via affinity chromatography and identified via mass spectrometry. We found evidence of spontaneous chimericity for four of the six protein assemblies tested and we showed that different types of complexes can cause a variety of phenotypes in selected environments. In the case of TRP2/TRP3 complex, the effect of such chimeric formation resulted in the fitness advantage of the hybrid in an environment lacking tryptophan...

## ‣ Evolutionary models for simple biosystems

Bagnoli, Franco
Tipo: Artigo de Revista Científica
Português
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The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of such systems has shown that indeed, systems under a flux of energy or matter can self-organize into complex patterns, think for instance to Rayleigh-Bernard convection, Liesegang rings, patterns formed by granular systems under shear. Following this line, one could characterize life as a state of matter, characterized by the slow, continuous process that we call evolution. In this paper we try to identify the organizational level of life, that spans several orders of magnitude from the elementary constituents to whole ecosystems. Although similar structures can be found in other contexts like ideas (memes) in neural systems and self-replicating elements (computer viruses, worms, etc.) in computer systems, we shall concentrate on biological evolutionary structure, and try to put into evidence the role and the emergence of network structure in such systems.; Comment: new version

## ‣ Fixation in Evolutionary Games under Non-Vanishing Selection

Mobilia, Mauro; Assaf, Michael
Tipo: Artigo de Revista Científica
Português
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One of the most striking effect of fluctuations in evolutionary game theory is the possibility for mutants to fixate (take over) an entire population. Here, we generalize a recent WKB-based theory to study fixation in evolutionary games under non-vanishing selection, and investigate the relation between selection intensity w and demographic (random) fluctuations. This allows the accurate treatment of large fluctuations and yields the probability and mean times of fixation beyond the weak selection limit. The power of the theory is demonstrated on prototypical models of cooperation dilemmas with multiple absorbing states. Our predictions compare excellently with numerical simulations and, for finite w, significantly improve over those of the Fokker-Planck approximation.; Comment: 4 figures, to appear in EPL (Europhysics Letters)

## ‣ Monotonicity of Fitness Landscapes and Mutation Rate Control

Belavkin, Roman V.; Channon, Alastair; Aston, Elizabeth; Aston, John; Krasovec, Rok; Knight, Christopher G.
Tipo: Artigo de Revista Científica
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The typical view in evolutionary biology is that mutation rates are minimised. Contrary to that view, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Ronald Fisher's work is the basis of much biological theory in this area. He used Euclidean geometry of continuous, infinite phenotypic spaces to study the relation between mutation size and expected fitness of the offspring. Here we develop a general theory of optimal mutation rate control that is based on the alternative geometry of discrete and finite spaces of DNA sequences. We define the monotonic properties of fitness landscapes, which allows us to relate fitness to the topology of genotypes and mutation size. First, we consider the case of a perfectly monotonic fitness landscape, in which the optimal mutation rate control functions can be derived exactly or approximately depending on additional constraints of the problem. Then we consider the general case of non-monotonic landscapes. We use the ideas of local and weak monotonicity to show that optimal mutation rate control functions exist in any such landscape and that they resemble control functions in a monotonic landscape at least in some neighbourhood of a fitness maximum. Generally...

## ‣ Analysis of the expected density of internal equilibria in random evolutionary multi-player multi-strategy games

Duong, Manh Hong; Han, The Anh
Tipo: Artigo de Revista Científica
Português
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In this paper, we study the distribution and behaviour of internal equilibria in a $d$-player $n$-strategy random evolutionary game where the game payoff matrix is generated from normal distributions. The study of this paper reveals and exploits interesting connections between evolutionary game theory and random polynomial theory. The main novelties of the paper are some qualitative and quantitative results on the expected density, $f_{n,d}$, and the expected number, $E(n,d)$, of (stable) internal equilibria. Firstly, we show that in multi-player two-strategy games, they behave asymptotically as $\sqrt{d-1}$ as $d$ is sufficiently large. Secondly, we prove that they are monotone functions of $d$. We also make a conjecture for games with more than two strategies. Thirdly, we provide numerical simulations for our analytical results and to support the conjecture. As consequences of our analysis, some qualitative and quantitative results on the distribution of zeros of a random Bernstein polynomial are also obtained.; Comment: 30 pages. Note that there was an error in the proof of Theorem 3.13 in the previous version. Please check the latest one

## ‣ EM for phylogenetic topology reconstruction on non-homogeneous data

Ibáñez, Esther; Casanellas, Marta
Tipo: Artigo de Revista Científica
Português
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Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly dealing with the long-branch attraction problem. The correct reconstruction of 4-taxon trees is crucial for making quartet-based methods work and being able to recover large phylogenies. Results: In this paper we consider an expectation-maximization method for maximizing the likelihood of (time nonhomogeneous) evolutionary Markov models on trees. We study its success on reconstructing 4-taxon topologies and its performance as input method in quartet-based phylogenetic reconstruction methods such as QFIT and QuartetSuite. Our results show that the method proposed here outperforms neighbor-joining and the usual (time-homogeneous continuous-time) maximum likelihood methods on 4-leaved trees with among-lineage instantaneous rate heterogeneity, and perform similarly to usual continuous-time maximum-likelihood when data satisfies the assumptions of both methods. Conclusions: The method presented in this paper is well suited for reconstructing the topology of any number of taxa via quartet-based methods and is highly accurate...

## ‣ The mechanics of stochastic slowdown in evolutionary games

Altrock, Philipp M.; Traulsen, Arne; Galla, Tobias