Marcus A. M. de Aguiar

Marcus A. M. de Aguiar
University of Campinas | UNICAMP · Instituto de Física "Gleb Wataghin" (IFGW)

Doctor of Philosophy

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229
Publications
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3,292
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Publications

Publications (229)
Preprint
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The Kuramoto model describes the synchronization of coupled oscillators that have different natural frequencies. Among the many generalizations of the original model, Kuramoto and Sakaguchi (KS) proposed a {\it frustrated} version that resulted in dynamic behavior of the order parameter, even when the average natural frequency of the oscillators is...
Preprint
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Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here we consider a two...
Preprint
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Micro-evolutionary processes acting in populations and communities ultimately produce macro-evolutionary patterns. However, current models of species life histories -- including processes of speciation, persistence, hybridization, and eventual extinction -- rarely connect these two time scales. This leaves us with a limited theoretical understandin...
Article
Full-text available
Kuramoto’s original model describes the dynamics and synchronization behavior of a set of interacting oscillators represented by their phases. The system can also be pictured as a set of particles moving on a circle in two dimensions, which allows a direct generalization to particles moving on the surface of higher dimensional spheres. One of the k...
Preprint
Full-text available
Kuramoto's original model describes the dynamics and synchronization behavior of a set of interacting oscillators represented by their phases. The system can also be pictured as a set of particles moving on a circle in two dimensions, which allows a direct generalization to particles moving on the surface of higher dimensional spheres. One of the k...
Article
Full-text available
Mutation and drift play opposite roles in genetics. While mutation creates diversity, drift can cause gene variants to disappear, especially when they are rare. In the absence of natural selection and migration, the balance between the drift and mutation in a well-mixed population defines its diversity. The Moran model captures the effects of these...
Article
Full-text available
The dynamics of large systems of coupled oscillators is a subject of increasing importance with prominent applications in several areas such as physics and biology. The Kuramoto model, where a set of oscillators move around a circle representing their phases, is a paradigm in this field, exhibiting a continuous transition between disordered and syn...
Article
Full-text available
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains...
Preprint
Full-text available
Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains...
Preprint
Full-text available
Mutation and drift play opposite roles in genetics. While mutation creates diversity, drift can cause gene variants to disappear, especially when they are rare. In the absence of natural selection and migration, the balance between the drift and mutation in a well-mixed population defines its diversity. The Moran model captures the effects of these...
Preprint
Full-text available
The dynamics of large systems of coupled oscillators is a subject of increasing importance with prominent applications in several areas such as physics and biology. The Kuramoto model, where a set of oscillators move around a circle representing their phases, is a paradigm in this field, exhibiting a continuous transition between disordered and syn...
Book
The International Conference on Complex Systems (ICCS) offers a unique interdisciplinary venue for researchers from the physical and biological sciences, social sciences, psychology and cognitive science, engineering, medicine, human systems, and global systems. This proceedings volume gathers selected papers from the conference. The New England C...
Preprint
Full-text available
Mitochondrial genetic material is widely used for phylogenetic reconstruction and as a barcode for species identification. Here we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nucl...
Article
Full-text available
The COVID-19 pandemic led several countries to resort to social distancing, the only known way to slow down the spread of the virus and keep the health system under control. Here we use an individual based model (IBM) to study how the duration, start date and intensity of quarantine affect the height and position of the peak of the infection curve....
Preprint
Full-text available
Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of phylogenies. Recently a new proposal has been introduced, based on the spectrum of the Laplacian matrix associ...
Preprint
Full-text available
The study of species organization and their clustering by genetic or phenotypic similarity is carried out with the tools of phylogenetic trees. An important structural property of phylogenetic trees is the balance, which measures how taxa are distributed among clades. Tree balance can be measured using indices such as the Sackin ($S$) and the Total...
Article
Full-text available
The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact directly with each other and indirectly through environmental effects, however to our knowledge the role of these ecosystem engineers has not been considered in ecological network models. H...
Article
Full-text available
The shape of a phylogenetic tree is defined by the sequence of speciation events, represented by its branching points, and extinctions, represented by branch interruptions. In a neutral scenario of parapatry and isolation by distance, species tend to branch off the original population one after the other, leading to highly unbalanced trees. In this...
Article
Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speci...
Preprint
Full-text available
The COVID-19 pandemic led several countries to resort to social distancing, the only known way to slow down the spread of the virus and keep the health system under control. Here we use an individual based model (IBM) to study how the duration, start date and intensity of quarantine affect the height and position of the peak of the infection curve....
Article
Swarmalators are particles that exhibit coordinated motion and, at the same time, synchronize their intrinsic behavior, represented by internal phases. Here, we study the effects produced by an external periodic stimulus over a system of swarmalators that move in two dimensions. The system represents, for example, a swarm of fireflies in the presen...
Article
Full-text available
Biodiversity loss is a hallmark of our times, but predicting its consequences is challenging. Ecological interactions form complex networks with multiple direct and indirect paths through which the impacts of an extinction may propagate. Here we show that accounting for these multiple paths connecting species is necessary to predict how extinctions...
Preprint
Full-text available
Although geographic isolation has been shown to play a key role in promoting reproductive isolation, it is now believed that speciation can also happen in sympatry and with considerable gene flow. Here we present a model of sympatric speciation based on assortative mating that does not require a genetic threshold for reproduction, i.e., that does n...
Preprint
Full-text available
Swarlamators are particles capable of synchronize and swarm. Here we study the effects produced by an external periodic stimulus over a system of swarmalators that move in two dimensions. When the particles are fixed and interact with equal strength (Kuramoto oscillators) their phases tend to synchronize and lock to the external stimulus if its int...
Article
Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly hetero...
Preprint
Full-text available
The complexity of an ecological community can be distilled into a network, where diverse interactions connect species in a web of dependencies. Species interact not only with each other but indirectly through environmental effects, however the role of these ecosystem engineers has not yet been considered in models of ecological networks. Here we ex...
Article
The spatial distribution of populations can influence the evolutionary outcome of species inter- actions. The variation in direction and strength of selection across local communities creates geographic selection mosaics that, when combined with gene flow and genomic processes such as genome duplication or hybridization, can fuel ongoing coevolutio...
Preprint
Full-text available
Synchronization plays a key role in information processing in neuronal networks. Response of specific groups of neurons are triggered by external stimuli, such as visual, tactile or olfactory inputs. Neurons, however, can be divided into several categories, such as by physical location, functional role or topological clustering properties. Here we...
Article
Full-text available
We study an influence network of voters subjected to correlated disordered external perturbations, and solve the dynamical equations exactly for fully connected networks. The model has a critical phase transition between disordered unimodal and ordered bimodal distribution states, characterized by an increase in the vote-share variability of the eq...
Article
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating ra...
Article
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem we analysed a spatially-explicit model of speciation where genome size and mating ra...
Article
Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of pattern...
Preprint
Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. Thes...
Article
We study the synchronization of Kuramoto oscillators on networks where only a fraction of them is subjected to a periodic external force. When all oscillators receive the external drive the system always synchronize with the periodic force if its intensity is sufficiently large. Our goal is to understand the conditions for global synchronization as...
Preprint
Social influence plays an important role in human behavior and decisions. Sources of influence can be divided as external, which are independent of social context, or as originating from peers, such as family and friends. An important question is how to disentangle the social contagion by peers from external influences. While a variety of experimen...
Article
Full-text available
A certain degree of inhibition is a common trait of dynamical networks in nature, ranging from neuronal and biochemical networks, to social and technological networks. We study here the role of inhibition in a representative dynamical network model, characterizing the dynamics of random threshold networks with both excitatory and inhibitory links....
Article
Full-text available
Phylogenetic trees are systematic tools to describe relatedness among species. The inference of biological trees aims to find the best phylogenetic tree that reconstructs the evolution of a group of species. Computer models that simulate the speciation process can track population dynamics and record information about genealogic relationships. In t...
Article
Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes). These issues may affect the accuracy of empirically constructed ecological networks. We e...
Article
According to apparent competition theory, the co-occurrence of two species that share the same predators appears to affect each other's population growth and abundance. However, due to habitat loss and over-hunting, top predators are being made rare worldwide. Considering that apparent competitors share similar resources, we would expect the absenc...
Article
Full-text available
Social influence plays an important role in human behavior and decisions. Sources of influence can be divided as external, which are independent of social context, or as originating from peers, such as family and friends. An important question is how to disentangle the social contagion by peers from external influences. While a variety of experimen...
Data
Hot spot analysis of social influence: 1920 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1940 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1948 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1952 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1972 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hotspots of social contagion: 92 years of presidential elections. S1 Movie shows colored maps that reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic. This analysis was perform...
Data
Hot spot analysis of social influence: 1960 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1984 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1988 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Results of random permutation tests of spatial autocorrelation using Moran’s I statistic. This analysis was performed with a contiguity spatial weight matrix (row normalized) that indicates whether states share a boundary or not. The variable of concern is the social influence index calculated using Eq 7 in the main text. The observed Moran’s I sta...
Data
Testing for a break in the level of social influence using the Mann-Whiney U-test. The Mann—Whitney U-test is a nonparametric test that assesses whether one of two random variables is stochastically larger than the other. Given a time-series of social influence from 1920 to 2012, we define for each election year, y, two samples of social influence:...
Data
Hot spot analysis of social influence: 1924 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1932 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1936 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1956 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1968 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1980 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1992 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Social influence topography of the United States: 1920–2012. S2 Movie shows maps of social influence for all election years. The colored areas are derived from the social influence index calculated using Eq 7 in the main text. (MOV)
Data
Hot spot analysis of social influence: 1928 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1944 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1964 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1976 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 1996 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 2000 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 2008 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 2012 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Hot spot analysis of social influence: 2004 US presidential election. The colored areas reflect the significance (p-value) of local concentration of social influence for each state. The p-values for each state are derived from a random permutation test of local clustering using the Getis-Ord Local Gi* statistic (see Fig 5 in main text for details)....
Data
Results of random permutation tests of spatial clustering using Getis-Ord General G* statistic. This analysis was performed with a contiguity spatial weight matrix that indicates whether states share a boundary or not. The variable of concern is the social influence index calculated using Eq 7 in the main text. The observed Getis-Ord General G* sta...
Article
Interspecific interactions are affected by community context and, as a consequence, show spatial variation in magnitude and sign. The selective forces imposed by interactions at the mutualism-antagonism interface are a consequence of the traits involved and their matching between species. If mutualistic and antagonistic communities are linked by ge...
Article
Polymorphisms are usually associated with defenses and mating strategies, affecting the individual's fitness. Coexistence of different morphs is, therefore, not expected, since the fittest morph should outcompete the others. Nevertheless, coexistence is observed in many natural systems. For instance, males of the side-blotched lizards (Uta stansbur...
Article
Full-text available
Ring species are groups of organisms that dispersed along a ring shaped region in such a way that the two ends of the population which meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here we simulate the evolution of ring species assuming that indi...
Article
Full-text available
Social influence plays an important role in human behavior and decisions. The sources of influence can be generally divided into external, which are independent of social context, or as originating from peers, such as family and friends. An important question is how to disentangle the social contagion by peers from external influences. While a vari...
Article
The dynamics of coevolution is a spatio-temporal process that cannot be understood by mean field approximations, where populations are considered well mixed and interactions are random. This intrinsic characteristic makes comprehensive empirical studies difficult and computer simulations can help to understand the interplay between the many compone...
Article
Full-text available
The speciation model proposed by Derrida and Higgs demonstrated that a sexually reproducing population can split into different species in the absence of natural selection or any type of geographic isolation, provided that mating is assortative and the number of genes involved in the process is infinite. Here we revisit this model and simulate it f...
Article
We study the motion of a composite particle in a one-dimensional billiard with a moving wall. The particle is modelled by two point masses coupled by a harmonic spring. We show that the energy gained by the composite particle is greatly reduced with respect to a single point particle. We show that the amount of energy transferred to the system at e...
Article
Full-text available
In finite populations the action of neutral mutations is balanced by genetic drift, leading to a stationary distribution of alleles that displays a transition between two different behaviors. For small mutation rates most individuals will carry the same allele at equilibrium, whereas for high mutation rates the alleles will be randomly distributed...