Quantitative Biology - Populations and Evolution Publications (50)

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Quantitative Biology - Populations and Evolution Publications

For decades, dengue virus has been a cause of major public health concern in Costa Rica, due to its landscape and climatic conditions that favor the circumstances in which the vector, Aedes aegypti, thrives. The emergence and introduction throughout tropical and subtropical countries of the chikungunya virus, as of 2014, challenged Costa Rican health authorities to provide a correct diagnosis since it is also transmitted by the same vector and infected hosts may share similar symptoms. We study the 2015-2016 dengue and chikungunya outbreaks in Costa Rica while establishing how point estimates of epidemic parameters for both diseases compare to one another. Read More


We are living in an uncertain and dynamically changing world. Under uncertainty, perception of risk is an important factor for value-based decision-making and it is directly linked to the survival of species. However, how evolutionary selection pressures might have shaped risk attitudes in the population received almost no attention. Read More


In this paper, a brief review of delay population models and their applications in ecology is provided. The inclusion of diffusion and nonlocality terms in delay models has given more capabilities to these models enabling them to capture several ecological phenomena such as the Allee effect, waves of invasive species and spatio-temporal competitions of interacting species. Moreover, recent advances in the studies of traveling and stationary wave solutions of delay models are outlined. Read More


While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). Read More


Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. On general grounds, highly connected individuals and sites exposed to the infection have similar roles in the epidemic propagation. Motivated by this feature, we propose a novel vaccination scheme that exploits information from the details of the infection pattern at the vaccination time. Read More


The provision of intergenerational care, via the Grandmother Hypothesis, has been implicated in the evolution of post-fertile longevity, particularly in humans. However, if grandmothering does provide fitness benefits, a key question is why has it evolved so infrequently? We investigate this question with a combination of life-history and evolutionary game theory. We derive simple eligibility and stability thresholds, both of which must be satisfied if intergenerational care is first to evolve and then to persist in a population. Read More


The emergence and survival of cooperation is one of the hardest problems still open in science. Several factors such as the existence of punishment, fluctuations in finite systems, repeated interactions and the formation of prestige may all contribute to explain the counter-intuitive prevalence of cooperation in natural and social systems. The characteristics of the interaction networks have been also signaled as an element favoring the persistence of cooperators. Read More


In this paper, we study how the pro-social impact due to the vigilance by other individuals is conditioned by both environmental and evolutionary effects. To this aim, we consider a known model where agents play a Prisoner's Dilemma Game (PDG) among themselves and the pay-off matrix of an individual changes according to the number of neighbors that are "vigilant", i.e. Read More


For animals living in groups, one of the important questions is to understand what are the decision-making mechanisms that lead to choosing a motion direction or leaving an area while preserving group cohesion. Here, we analyse the initiation of collective departure in zebrafish \textit{Danio rerio}. In particular, we observed groups of 2, 3, 5, 7 and 10 zebrafish swimming in a two resting sites arena and quantify the number of collective departure initiated by each fish. Read More


The segregation of plasmids in a bacterial population is investigated. Hereby, a dynamical model is formulated in terms of a size-structured population using a hyperbolic partial differential equation incorporating non-local terms (the fragmentation equation). For a large class of parameter functions this PDE can be re-written as an infinite system of ordinary differential equations for the moments of its solution. Read More


Genetic drift is stochastic fluctuations of alleles frequencies in a population due to sampling effects. We consider a model of drift in an equilibrium population, with high mutation rates: few functional mutations per generation. Such mutation rates are common in multicellular organisms including humans, however they are not explicitly considered in most population genetics models. Read More


This thesis focuses on the applications of mathematical tools and concepts brought from nonequilibrium statistical physics to the modeling of ecological problems. The first part provides a short introduction where the theoretical concepts and mathematical tools that are going to be used in subsequent chapters are presented. Firstly, the different levels of description usually employed in the models are explained. Read More


We study the influence of the complex topology of scale-free graphs on the dynamics of anti-coordination games (snowdrift games). These reference models are characterized by the coexistence (evolutionary stable mixed strategy) of two competing species, say "cooperators" and "defectors", and, in finite systems, by metastability and by large-fluctuation-driven fixation. Here, we analyze how the complex scale-free topology affects these properties. Read More


We explore the collective behaviours of 7 group sizes: 1, 2, 3, 5, 7, 10 and 20 AB zebrafish (Danio rerio) in a constraint environment composed of two identical squared rooms connected by a corridor. This simple set-up is similar to a natural patchy environment. We track the positions and the identities of the fish and compute the metrics at the group and at the individual levels. Read More


Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the inevitable cost associated to detecting environmental cues and responding to them in adaptive ways, we conjecture that the potential for predicting the environment can overcome the expenses associated to maintaining costly, complex structures. We present a minimal formal model grounded in information theory and selection, in which successive generations of agents are mapped into transmitters and receivers of a coded message. Read More


Agent-based models (ABMs) simulate interactions between autonomous agents in constrained environments over time. ABMs are often used for modeling the spread of infectious diseases. In order to simulate disease outbreaks or other phenomena, ABMs rely on "synthetic ecosystems," or information about agents and their environments that is representative of the real world. Read More


To be able to understand how infectious diseases spread on networks, it is important to understand the network structure itself in the absence of infection. In this text we consider dynamic network models that are inspired by the (static) configuration network. The networks are described by population-level averages such as the fraction of the population with $k$ partners, $k=0,1,2,\ldots$ This means that the bookkeeping contains information about individuals and their partners, but no information about partners of partners. Read More


Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the host's molecular resources, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely T4 and influenza. Read More


Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along which these networks evolve but any other one-dimensional gradient (temperature, altitude, depth, humidity, . Read More


To introduce selection into a model of coalescence, I explore the use of modified integer partitions that allow the identification of a preferred lineage. I show that a partition-partition transition matrix, along with Monte Carlo discrete time kinetics, treats both the neutral case and a wide range of positive and negative selection pressures for small population sizes. Selection pressure causes multiple collisions per generation, short coalescence times, increased lengths of terminal branches, increased tree asymmetry, and dependence of coalescence times on the logarithm of population size. Read More


How can tissues generate large numbers of cells, yet keep the divisional load (the number of divisions along cell lineages) low in order to curtail the accumulation of somatic mutations and reduce the risk of cancer? To answer the question we consider a general model of hierarchically organized self-renewing tissues and show that the lifetime divisional load of such a tissue is independent of the details of the cell differentiation processes, and depends only on two structural and two dynamical parameters. Our results demonstrate that a strict analytical relationship exists between two seemingly disparate characteristics of self-renewing tissues: divisional load and tissue organization. Most remarkably, we find that a sufficient number of progressively slower dividing cell types can be almost as efficient in minimizing the divisional load, as non-renewing tissues. Read More


Biological functions are typically performed by groups of cells that express predominantly the same genes, yet display a continuum of phenotypes. While it is known how one genotype can generate such non-genetic diversity, it remains unclear how different phenotypes contribute to the performance of biological function at the population level. We developed a microfluidic device to simultaneously measure the phenotype and chemotactic performance of tens of thousands of individual, freely-swimming Escherichia coli as they climbed a gradient of attractant. Read More


Biological species have to cope with stochastic variations in both the external environment and the internal population dynamics. Theoretical studies and laboratory experiments suggest that population diversification could be an effective bet-hedging strategy for adaptation to temporally varying environments. Here we show that bet-hedging can also be effective against demographic fluctuations that cause extinction of local populations. Read More


We propose a bio-inspired, agent-based approach to describe the natural phenomenon of group chasing in both two and three dimensions. Using a set of local interaction rules we created a continuous-space and discrete-time model with time delay, external noise and limited acceleration. We implemented a unique collective chasing strategy, optimized its parameters and studied its properties when chasing a much faster, erratic escaper. Read More


Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the elucidation of the relationships of individual specimens particularly important. Recent estimates of the phylogeny of key specimens include Waddell (2013, 2014, 2015, 2016), and Mounier et al. Read More


Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. Read More


Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m (1 - 1/(2N)))$, where $m$ is a Malthusian fitness and $N_e$ and $N$ are the effective and actual population sizes. Combining this finding with the knowledge of protein folding, we derive a correspondence between protein fitness and folding free energy, i.e. Read More


The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where the total interaction $\psi_N$ is represented as the sum of one body and pairwise interactions. A protein folding theory based on the random energy model (REM) indicates that the equilibrium ensemble of natural protein sequences is a canonical ensemble characterized by $\exp(-\Delta G_{ND}/k_B T_s)$ or by $\exp(- G_{N}/k_B T_s)$ if an amino acid composition is kept constant, meaning $\psi_N = \Delta G_{ND}/k_B T_s +$ constant, where $\Delta G_{ND} \equiv G_N - G_D$, $G_N$ and $G_D$ are the native and denatured free energies, and $T_s$ is the effective temperature of natural selection. Here, we examine interaction changes ($\Delta \psi_N$) due to single nucleotide nonsynonymous mutations, and have found that the variance of their $\Delta \psi_N$ over all sites hardly depends on the $\psi_N$ of each homologous sequence, indicating that the variance of $\Delta G_N (= k_B T_s \Delta \psi_N)$ is nearly constant irrespective of protein families. Read More


Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation, and human-driven habitat degradation. Such threats are pushing ecosystems to the brink of collapse. Because of a general presence of multiple stable states, including states involving population extinction, and due to intrinsic nonlinearities associated with feedback loops, collapse can occur in a catastrophic manner. Read More


In Nature microbial populations are subject to fluctuating nutrient levels. Nutrient abundance fluctuations are important for evolutionary and ecological dynamics in microbial communities since they impact growth rates, population sizes and microbial physiology. Here we use automated continuous-culture devices and single-cell imaging to show that when populations of Escherichia coli are subject to cycles of nutrient excess (feasts) and scarcity (famine) that their growth rate during feasts depends on their history of exposure to famine. Read More


We show, within the context of the standard class of deterministic ODE predator-prey mathematical models, that predator culling does not produce a long term decrease in the predator population. Read More


The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these aptamers through evolutionary selection of high-affinity candidates from a highly diverse random pool. This randomness dictates an unknown population distribution of fitness parameters, encoded by the binding affinities, toward SELEX targets. Read More


Game theory research on the snowdrift game has showed that gradual evolution of the continuously varying level of cooperation in joint enterprises can demonstrate evolutionary merging as well as evolutionary branching. However, little is known about the consequences of changes in diversity at the cooperation level. In the present study I consider effects of costly rewards on the continuous snowdrift game. Read More


Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Read More


We present a computational model to reconstruct ancestor trees of animals with sexual reproduction following the theoretical model presented in \textit{Phys. Rev. E} \textbf{90}, 022125 (2014). Read More


Measures of wealth and production have been found to scale superlinearly with the population of a city. Therefore, it makes economic sense for humans to congregate together in dense settlements. A recent model of population dynamics showed that population growth can become superexponential due to the superlinear scaling of production with population in a city. Read More


Microbial populations undergo multiple phases of growth, including a lag phase, an exponential growth phase, and a stationary phase. Therefore mutations can improve the frequency of a genotype not only by increasing its growth rate, but also by decreasing the lag time or adjusting the yield (resource efficiency). Furthermore, many mutations will be pleiotropic, affecting multiple phases simultaneously. Read More


The view that the initiation of branching into two sympatric species may not require natural selection emerged in Victorian times (Fleeming Jenkin, George Romanes, William Bateson). In the 1980s paleontologist Steven Jay Gould gave a theoretical underpinning of this non-genic "chromosomal" view, thus reinstating Richard Goldschmidt's "heresy" of the 1930s. From modelling studies with computer-generated "biomorphs," zoologist Richard Dawkins also affirmed Goldschmidt, proclaiming the "evolution of evolvability. Read More


The paper deals with using chaos to direct trajectories to targets and analyzes ruggedness and fractality of the resulting fitness landscapes. The targeting problem is formulated as a dynamic fitness landscape and four different chaotic maps generating such a landscape are studied. By using a computational approach, we analyze properties of the landscapes and quantify their fractal and rugged characteristics. Read More


The consensus that complexity begets stability in ecosystems was challenged in the seventies, a result recently extended to ecologically-inspired networks. The approaches assume the existence of a feasible equilibrium, i.e. Read More


Species experience both internal feedbacks with endogenous factors such as trait evolution and external feedbacks with exogenous factors such as weather. These feedbacks can play an important role in determining whether populations persist or communities of species coexist. To provide a general mathematical framework for studying these effects, we develop a theorem for coexistence for ecological models accounting for internal and external feedbacks. Read More


Plasmodium vivax populations are more resistant to malaria control strategies than Plasmodium falciparum, maintaining high genetic diversity and gene flow even at low transmission. To quantify the impact of declining transmission on P. vivax populations, we investigated population genetic structure over time during intensified control efforts and over a wide range of transmission intensities and spatial scales in the Southwest Pacific. Read More


In the context of bacteria and models of their evolution under genome rearrangement, we explore a novel application of group representation theory to the inference of evolutionary history. Our contribution is to show, in a very general maximum likelihood setting, how to use elementary matrix algebra to sidestep intractable combinatorial computations and convert the problem into one of eigenvalue estimation amenable to standard numerical approximation techniques. Read More


It has been hypothesized that one of the main reasons evolution has been able to produce such impressive adaptations is because it has improved its own ability to evolve -- "the evolution of evolvability". Rupert Riedl, for example, an early pioneer of evolutionary developmental biology, suggested that the evolution of complex adaptations is facilitated by a developmental organization that is itself shaped by past selection to facilitate evolutionary innovation. However, selection for characteristics that enable future innovation seems paradoxical: natural selection cannot favor structures for benefits they have not yet produced, and favoring characteristics for benefits that have already been produced does not constitute future innovation. Read More


We study evolutionary multi-player games in finite populations, subject to fluctuating environments. The population undergoes a birth-death process with absorbing states, and the environment follows a Markovian process, resulting in a fluctuating payoff matrix for the evolutionary game. Our focus is on the fixation or extinction of a single mutant in a population of wildtypes. Read More


We generalize a model of growth over a disordered environment, to a large class of It\=o processes. In particular, we study how the microscopic properties of the noise influence the macroscopic growth rate. The present model can account for growth processes in large dimensions, and provides a bed to understand better the trade-off between exploration and exploitation. Read More


A two-types, discrete-time population model with finite, constant size is constructed, allowing for a general form of frequency-dependent selection and skewed offspring distribution. Selection is defined based on the idea that individuals first choose a (random) number of $\textit{potential}$ parents from the previous generation and then, from the selected pool, they inherit the type of the fittest parent. The probability distribution function of the number of potential parents per individual thus parametrises entirely the selection mechanism. Read More


The understanding of the macroscopic phenomenological models of the population growth at a microscopic level is important to predict the population behaviors emerged from the interactions between the individuals. In this work we consider the influence of the cell-cell interaction on the population growth rate $R$ in a tumor system, and show that, in most cases especially small proliferative probabilities, the regulative role of the interaction will be strengthened with the decline of the intrinsic proliferative probabilities. For the high replication rates of an individual and the cooperative interactions, the proliferative probability almost has no effect. Read More


Understanding the spread of any disease is a highly complex and interdisciplinary exercise as biological, social, geographic, economic, and medical factors may shape the way a disease moves through a population and options for its eventual control or eradication. Disease spread poses a serious threat in animal and plant health and has implications for ecosystem functioning and species extinctions as well as implications in society through food security and potential disease spread in humans. Space-time epidemiology is based on the concept that various characteristics of the pathogenic agents and the environment interact in order to alter the probability of disease occurrence and form temporal or spatial patterns. Read More