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Markovian approach to tackle the interaction of simultaneous diseasesJul 15 2019The simultaneous emergence of several abrupt disease outbreaks or the extinction of some serotypes of multi-strain diseases are fingerprints of the interaction between pathogens spreading within the same population. Here, we propose a general and versatile ... More
Caching in or falling back at the SevilletaJul 15 2019Foraging in uncertain environments requires balancing the risks associated with finding alternative resources against potential gains. In aridland environments characterized by extreme variation in the amount and seasonal timing of primary production, ... More
Large and Small Data Blow-Up Solutions in the Trojan Y Chromosome ModelJul 13 2019The Trojan Y Chromosome Strategy (TYC) is an extremely well investigated biological control method for controlling invasive populations with an XX-XY sex determinism. In \cite{GP12, WP14} various dynamical properties of the system are analyzed, including ... More
Properties for the Frechet Mean in Billera-Holmes-Vogtmann TreespaceJul 12 2019The Billera-Holmes-Vogtmann (BHV) space of weighted trees can be embedded in Euclidean space, but the extrinsic Euclidean mean often lies outside of treespace. Sturm showed that the intrinsic Frechet mean exists and is unique in treespace. This Frechet ... More
How range residency and long-range perception change encounter ratesJul 12 2019Encounter rates link movement strategies to intra- and inter-specific interactions, and therefore translate individual movement behavior into higher-level ecological processes. Indeed, a large body of interacting population theory rests on the law of ... More
Evolving complexity: how tinkering shapes cells, software and ecological networksJul 12 2019A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not reducible ... More
Fixation properties of rock-paper-scissors games in fluctuating populationsJul 11 2019Jul 12 2019Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, ... More
Fixation properties of rock-paper-scissors games in fluctuating populationsJul 11 2019Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, ... More
Distribution of outbreak sizes for SIR disease in finite populationsJul 11 2019We consider the spread of a Susceptible-Infected-Recovered (SIR) disease through finite populations and derive an expression for the final size distribution. Our derivation allows arbitrary distributions of the number of transmissions caused by an infected ... More
On the minimum value of the Colless index and the bifurcating trees that achieve itJul 11 2019Measures of tree balance play an important role in the analysis of phylogenetic trees. One of the oldest and most popular indices in this regard is the Colless index for rooted bifurcating trees, introduced by Colless (1982). While many of its statistical ... More
A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directionsJul 11 2019Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont ... More
On the probability of strain invasion in endemic settings: accounting for individual heterogeneity and control in multi-strain dynamicsJul 11 2019The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant pathogens are ignited ... More
Evaluating bird collision risk of a high-speed railway crossing the habitat of the crested ibis (Nipponia nippon) in Qinling Mountains, ChinaJul 10 2019Bird collisions with high-speed transport modes is a vital topic on vehicle safety and wildlife protection, especially when high-speed trains, with an average speed of 250km/h, have to run across the habitat of an endangered bird species. This paper evaluates ... More
Metabolite mediated modeling of microbial community dynamics captures emergent behavior more effectively than species-species modelingJul 09 2019Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling ... More
Making Study Populations Visible through Knowledge GraphsJul 09 2019Treatment recommendations within Clinical Practice Guidelines (CPGs) are largely based on findings from clinical trials and case studies, referred to here as research studies, that are often based on highly selective clinical populations, referred to ... More
Optimal Control and Analysis of a Modified Trojan Y-Chromosome StrategyJul 08 2019The Trojan Y Chromosome (TYC) Strategy is a promising eradication method that attempts to manipulate the female to male ratio to promote the reduction of the population of an invasive species. The manipulation stems from an introduction of sex-reversed ... More
How many groups? A statistical methodology for data-driven partitioning of infectious disease incidence into age-groupsJul 08 2019Understanding age-group dynamics of infectious diseases is a fundamental issue for both scientific study and policymaking. Age-structure epidemic models were developed in order to study and improve our understanding of these dynamics. By fitting the models ... More
Social inhibition maintains adaptivity and consensus of foraging honeybee swarms in dynamic environmentsJul 06 2019To effectively forage in natural environments, organisms must adapt to changes in the quality and yield of food sources across multiple timescales. Individuals foraging in groups act based on both their private observations and the opinions of their neighbors. ... More
Dominance, Sharing, and Assessment in an Iterated Hawk--Dove GameJul 03 2019Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting ... More
Evolution of cooperation driven by active information spreadingJul 03 2019Cooperators forgo their interest to benefit others. Thus cooperation should not be favored by natural selection. It challenges the evolutionists, since cooperation is widespread. As one of the resolutions, information spreading has been revealed to play ... More
Model of pattern formation in marsh ecosystems with nonlocal interactionsJul 03 2019Smooth cordgrass Spartina alterniflora is a grass species commonly found in tidal marshes. It is an ecosystem engineer, capable of modifying the structure of its surrounding environment through various feedbacks. The scale-dependent feedback between marsh ... More
Being a leader or being the leader: The evolution of institutionalised hierarchyJul 03 2019Human social hierarchy has the unique characteristic of existing in two forms. Firstly, as an informal hierarchy where leaders and followers are implicitly defined by their personal characteristics, and secondly, as an institutional hierarchy where leaders ... More
Gradient flow formulations of discrete and continuous evolutionary models: a unifying perspectiveJul 02 2019We consider three classical models of biological evolution: (i) the Moran process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator Equation, a paradigm ... More
Modelling the evolution of traits in a two-sex population, with an application to grandmotheringJul 02 2019We present a mathematical simplification for the evolutionary dynamics of a heritable trait within a two-sex population. This trait is assumed to control the timing of sex-specific life-history events, such as the age of sexual maturity and end of female ... More
Representing fitness landscapes by valued constraints to understand the complexity of local searchJul 02 2019Local search is widely used to solve combinatorial optimisation problems and to model biological evolution, but the performance of local search algorithms on different kinds of fitness landscapes is poorly understood. Here we introduce a natural approach ... More
Climate-induced intermittent response of the population boundary across an environmental gradient: effects of quenched disorderJul 01 2019Climatic response of population boundaries, known as ecotone, is a classic indicator in ecology. In addition to known challenges, the spatial and dynamical characteristics of the boundary are not only affected by the spatial gradient in the environmental ... More
A Data-Validated Host-Parasite Model for Infectious Disease OutbreaksJun 29 2019The use of model experimental systems and mathematical models is important to further understanding of infectious disease dynamics and strategize disease mitigation. Gyrodactylids are helminth ectoparasites of teleost fish which have many dynamical characteristics ... More
Multistability and regime shifts in microbial communities explained by competition for essential nutrientsJun 29 2019Microbial communities routinely have several possible species compositions or community states observed for the same environmental parameters. Changes in these parameters can trigger abrupt and persistent transitions (regime shifts) between such community ... More
Generating Normal Networks via Leaf Insertion and Nearest Neighbor InterchangeJun 28 2019Jul 01 2019Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition. Although these ... More
Why does women's fertility end in mid-life? Grandmothering and age at last birthJun 28 2019Great apes, the other living members of our hominid family, become decrepit before the age of forty and rarely outlive their fertile years. In contrast, women - even in high mortality hunter-gatherer populations - usually remain healthy and productive ... More
Evolution of longevity, age at last birth and sexual conflict with grandmotheringJun 28 2019We use a two-sex partial differential equation (PDE) model based on the Grandmother Hypothesis. We build on an earlier model by Kim et al. [27] by allowing for evolution in both longevity and age at last birth, and also assuming that post-fertile females ... More
Dynamics of Social Interactions and Agent Spreading in Social Insects Colonies: Effects of Environmental Events and Spatial HeterogeneityJun 28 2019The relationship between division of labor and individuals' spatial behavior in social insect colonies provides a useful context to study how social interactions influence the spreading of agent (which could be information or virus) across distributed ... More
Conformity bias in the cultural transmission of music sampling traditionsJun 27 2019One of the fundamental questions of cultural evolutionary research is how individual-level processes scale up to generate population-level patterns. Previous studies in music have revealed that frequency-based bias (e.g. conformity and novelty) drives ... More
Tuning environmental timescales to evolve and maintain generalistsJun 27 2019Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such `generalists' can be hard to evolve, out-competed by specialists fitter in any particular environment. Here, inspired by the search for broadly-neutralising ... More
The minimal observable clade size of exchangeable coalescentsJun 27 2019For $\Lambda$-$n$-coalescents with mutation, we analyse the size $O_n$ of the partition block of $i\in\{1,\ldots,n\}$ at the time where the first mutation appears on the tree that affects $i$ and is shared with any other $j\in\{1,\ldots,n\}$. We provide ... More
Horizontal gene transfer: numerical comparison between stochastic and deterministic approachesJun 27 2019Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that this phenomenon ... More
Dynamics of disease spread. Effect of the characteristic timesJun 27 2019Dynamic properties of spreading infection through a heterogeneous population are studied numerically and analytically using a dynamic variant of Watts and Strogatz Small World Network-based stochastic Susceptible-Exposed-Infectious-Removed (SEIR) epidemic ... More
Gut microbiome composition: back to baseline?Jun 27 2019In Nature Microbiology, Palleja and colleagues studied the changes in gut microbiome composition in twelve healthy men over a period of six months following an antibiotic intervention. The authors argued that the 'gut microbiota of the subjects recovered ... More
Network Inference from Population-Level Observation of EpidemicsJun 26 2019The network paradigm is widely accepted as the gold standard in modelling complex systems such as epidemics or neuronal activity in the brain; however, in most cases, the exact nature of the network on which such dynamics unfold is unknown. This has motivated ... More
The dual-process approach to human sociality: A reviewJun 24 2019Which social decisions are intuitive? Which are deliberative? The dual-process approach to human sociality has emerged in the last decades as a vibrant and exciting area of research. Here, I review the existing literature on the cognitive basis of cooperation, ... More
Evaluating the impact of PrEP on HIV and gonorrhea on a networked population of female sex workersJun 21 2019Sexual contacts are the main spreading route of HIV. This puts sex workers at higher risk of infection even in populations where HIV prevalence is moderate or low. Alongside condom use, Pre-Exposure Prophylaxis (PrEP) is an effective tool for sex workers ... More
Evaluating the impact of PrEP on HIV and gonorrhea on a networked population of female sex workersJun 21 2019Jul 02 2019Sexual contacts are the main spreading route of HIV. This puts sex workers at higher risk of infection even in populations where HIV prevalence is moderate or low. Alongside condom use, Pre-Exposure Prophylaxis (PrEP) is an effective tool for sex workers ... More
On the use of multiple compartment epidemiological models to describe the dynamics of influenza in EuropeJun 18 2019We develop a multiple compartment Susceptible-Infected-Recovered (SIR) model to analyze the spread of several infectious diseases through different geographic areas. Additionally, we propose a data-quality sensitive optimization framework for fitting ... More
Discrimination emerging through spontaneous symmetry breaking in a spatial prisoner's dilemma model with multiple labelsJun 18 2019Social discrimination seems to be a persistent phenomenon in many cultures. It is important to understand the mechanisms that lead people to judge others by the group to which they belong, rather than individual qualities. It was recently shown that evolutionary ... More
What drives Oregon shelf summer hypoxia?Jun 18 2019Using coupled biological-physical model based on NPZD-type biological model and 3D coastal ocean model (ROMS) we studied dissolved oxygen (DO) dynamics and hypoxia development on Oregon shelf during April-August of 2002, 2006, and 2008. We found that ... More
How heterogeneous thymic output and homeostatic proliferation shape naive T cell receptor clone abundance distributionsJun 18 2019The set of T cells that express the same T cell receptor (TCR) sequence represent a T cell clone. The number of different naive T cell clones in an organism reflects the number of different T cell receptors (TCRs) arising from recombination of the V(D)J ... More
Multi-lineage evolution in viral populations driven by host immune systemsJun 18 2019Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature include the effectively ... More
Rooting for phylogenetic networksJun 18 2019This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected binary phylogenetic network, given the locations of the root and ... More
Fitness differences suppress the number of mating types in evolving isogamous speciesJun 17 2019Sexual reproduction is not always synonymous with the existence of two morphologically different sexes; isogamous species produce sex cells of equal size, typically falling into multiple distinct self-incompatible classes, termed mating types. A long-standing ... More
Invariance in ecological patternJun 17 2019The abundance of different species in a community often follows the log series distribution. Other ecological patterns also have simple forms. Why does the complexity and variability of ecological systems reduce to such simplicity? Common answers include ... More
How tree-based is my network? Proximity measures for unrooted phylogenetic networksJun 14 2019Evolutionary events like hybridization and horizontal gene transfer cannot be represented by a tree but require a phylogenetic network instead. Nonetheless, it has been argued that evolution is fundamentally tree-like, in the sense that it can be modeled ... More
How tree-based is my network? Proximity measures for unrooted phylogenetic networksJun 14 2019Jun 24 2019Evolutionary events like hybridization and horizontal gene transfer cannot be represented by a tree but require a phylogenetic network instead. Nonetheless, it has been argued that evolution is fundamentally tree-like, in the sense that it can be modeled ... More
Global analysis of a predator-prey model with variable predator search rateJun 13 2019We consider a modified Rosenzweig-MacArthur predator-prey model, based on the premise that the search rate of predators is dependent on the prey density, rather than constant. A complete analysis of the global behavior of the model is presented, and shows ... More
Semantic Change and Semantic Stability: Variation is KeyJun 13 2019I survey some recent approaches to studying change in the lexicon, particularly change in meaning across phylogenies. I briefly sketch an evolutionary approach to language change and point out some issues in recent approaches to studying semantic change ... More
Quasi-Stationary Distributions and Resilience: What to get from a sample?Jun 13 2019We study a class of multi-species birth-and-death processes going almost surely to extinction and admitting a unique quasi-stationary distribution (qsd for short). When rescaled by $K$ and in the limit $K\to+\infty$, the realizations of such processes ... More
Quasi-Stationary Distributions and Resilience: What to get from a sample?Jun 13 2019Jun 14 2019We study a class of multi-species birth-and-death processes going almost surely to extinction and admitting a unique quasi-stationary distribution (qsd for short). When rescaled by $K$ and in the limit $K\to+\infty$, the realizations of such processes ... More
An SEIR Epidemic Model where Empirical Distribution of Incubation Period has Approximated by Coxian DistributionJun 13 2019In this work, we have developed a Coxian distributed SEIR model in incorporating an empirical incubation period since Coxian distribution approximately converges to any distribution. A basic reproduction number is found from the model. An application ... More
Absolute negative mobility in evolutionJun 13 2019We investigate a population-genetic model in a specific fluctuating environment. We numerically show that a counter-intuitive behavior occurs where fitness of the system decreases as selection pressure increases from zero. This phenomenon is understood ... More
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variationJun 12 2019Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence ... More
Relaxed random walks at scaleJun 11 2019Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny and more accurately model overdispersed biological data. Increased taxonomic ... More
Vaccination strategies to control Ebola epidemics in the context of variable household inaccessibility levelsJun 11 2019Jun 21 2019Despite a very effective vaccine, active conflict and community distrust during the ongoing DRC Ebola epidemic are undermining control efforts, including a ring vaccination strategy. However, 20% or more of close contacts cannot be reached or refused ... More
Vaccination strategies to control Ebola epidemics in the context of variable household inaccessibility levelsJun 11 2019Despite a very effective vaccine, active conflict and community distrust during the ongoing DRC Ebola epidemic are undermining control efforts, including a ring vaccination strategy. However, 20% or more of close contacts cannot be reached or refused ... More
Rearrangement operations on unrooted phylogenetic networksJun 11 2019Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), ... More
Altruism in populations at the extinction transitionJun 10 2019We study the evolution of cooperation as a birth-death process in spatially extended populations. The benefit from the altruistic behavior of a cooperator is implemented by decreasing the death rate of its direct neighbours. The cost of cooperation is ... More
Evolutionary Theory in Pacific Island ArchaeologyJun 10 2019Evolution is the principal theoretical framework in Pacific Island archaeology. Progressive cultural evolutionary stages, particularly the chiefdom, provided the earliest framework. These ideas were increasingly linked to islands as relatively isolated ... More
Evolutionary Theory in Pacific Island ArchaeologyJun 10 2019Jun 16 2019Evolution is the principal theoretical framework in Pacific Island archaeology. Progressive cultural evolutionary stages, particularly the chiefdom, provided the earliest framework. These ideas were increasingly linked to islands as relatively isolated ... More
Quantifying impacts of the drought 2018 on European ecosystems in comparison to 2003Jun 07 2019In recent decades, an increasing persistence of atmospheric circulation patterns has been observed. In the course of the associated long-lasting anticyclonic summer circulations, heat waves and drought spells often coincide, leading to so-called hotter ... More
Limits on amplifiers of natural selection under death-Birth updatingJun 06 2019The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous ... More
A partial order and cluster-similarity metric on rooted phylogenetic treesJun 06 2019Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in the neighbourhood ... More
Competitive Exclusion in a DAE Model for Microbial Electrolysis CellsJun 05 2019Microbial electrolysis cells (MECs) are devices that employ electroactive bacteria to perform extracellular electron transfer, enabling hydrogen generation from biodegradable substrates. Previously we analyzed a regular, semi-explicit, index 1 differential-algebraic ... More
Phylogenetic NetworksJun 04 2019Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these relationships. ... More
Dynamically generated hierarchies in games of competitionJun 04 2019Spatial many-species predator-prey systems have been shown to yield very rich space-time patterns. This observation begs the question whether there exist universal mechanisms for generating this type of emerging complex patterns in non-equilibrium systems. ... More
Mean field approximation of a heterogeneous population of plants in competitionJun 04 2019The processes of interplant competition within a field are still poorly understood. However, they explain a large part of the heterogeneity in a field and may have longer-term consequences, especially in mixed stands. Modeling can help to better understand ... More
Interacting contagions are indistinguishable from social reinforcementJun 04 2019From fake news to innovative technologies, many contagions spread via a process of social reinforcement, where multiple exposures are distinct from prolonged exposure to a single source. Contrarily, biological agents such as Ebola or measles are typically ... More
Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphsJun 03 2019The spatial structure of an evolving population affects which mutations become fixed. Some structures amplify selection, increasing the likelihood that beneficial mutations become fixed while deleterious mutations do not. Other structures suppress selection, ... More
Immunopathogenesis in Psoriasis through a Density-type Mathematical ModelJun 03 2019Disease psoriasis occurs as chronic inflammation of skin and appears as scaly red lesions on skin surface. Advent of several immunosuppressive drugs established that the disease stems from immuno-pathogenic disorder in human blood. Cell biological as ... More
Exact travelling solution for a reaction-diffusion system with a piecewise constant production supported by a codimension-1 subspaceJun 02 2019A generalisation of reaction diffusion systems and their travelling solutions to cases when the productive part of the reaction happens only on a surface in space or on a line on plane but the degradation and the diffusion happen in bulk are important ... More
Point mutations in a growing cell populationMay 29 2019A growing cell population such as cancer or bacteria accumulates point mutations (single nucleotide changes in DNA). To model this process, we consider that cells divide and die as a branching process, and that each cell contains a sequence of nucleotides ... More
Dynamics of T Cell Receptor Distributions Following Acute Thymic Atrophy and ResumptionMay 29 2019Naive human T cells are produced in the thymus, which atrophies abruptly and severely in response to physical or psychological stress. To understand how an instance of stress affects the size and "diversity" of the peripheral naive T cell pool, we derive ... More
Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogeneticsMay 29 2019Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional ... More
Evolutionary dynamics of competing phenotype-structured populations in periodically fluctuating environmentsMay 28 2019Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in ecology, which ... More
Exploring Evolving Plants as Interacting Particles in a Randomly Generated Heterogeneous EnvironmentMay 24 2019We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other attributes that ... More
Evolutionary dynamics with stochastic game transitionsMay 24 2019The environment has a strong influence on a population's evolutionary dynamics. Driven by both intrinsic and external factors, the environment is subject to continuous change in nature. To model an ever-changing environment, we develop a framework of ... More
A trust model for spreading gossip in social networksMay 23 2019We introduce here a multi-type bootstrap percolation model, which we call T-Bootstrap Percolation (T-BP), and apply it to study information propagation in social networks. In this model, a social network is represented by a graph G whose vertices have ... More
Estimation of black bear abundance by management zone in WisconsinMay 22 2019Estimates of population abundance are fundamental to wildlife management and conservation, but are difficult to obtain across large geographic scales and for cryptic species. We used a state-space model with age-at-harvest data in a Bayesian framework ... More
Evolving nature of human contact networks with its impact on epidemic processesMay 21 2019Human contact networks are constituted by a multitude of individuals and pairwise contacts among them. However, the dynamic nature, which generates the evolution of human contact networks, of contact patterns is not known yet. Here, we analyse three empirical ... More
The Stabilisation of Equilibria in Evolutionary Game Dynamics through Mutation: Mutation Limits in Evolutionary GamesMay 20 2019The multi-population replicator dynamics (RD) can be considered a dynamic approach to the study of multi-player games, where it was shown to be related to Cross' learning, as well as of systems of coevolving populations. However, not all of its equilibria ... More
The network architecture of the human brain is modularly encoded in the genomeMay 18 2019The form of genotype-phenotype maps are typically modular. However, the form of the genotype-phenotype map in human brain connectivity is unknown. A modular mapping could exist, in which distinct sets of genes' coexpression across brain regions is similar ... More
Nestedness in complex networks: Observation, emergence, and implicationsMay 18 2019The observed architecture of ecological and socio-economic networks differs significantly from that of random networks. From a network science standpoint, non-random structural patterns observed in real networks call for an explanation of their emergence ... More
Pattern formation induced by intraspecific interactions in a predator-prey systemMay 17 2019Differential diffusion is a source of instability in population dynamics systems when species diffuse with different rates. Predator-prey systems show this instability only under certain specific conditions, usually requiring Holling-type functionals ... More
NANUQ: A method for inferring species networks from gene trees under the coalescent modelMay 16 2019Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but arise with frequencies ... More
Getting a head start: the slime mold, Physarum polycephalum, tune foraging decision to motivational asymmetry when faced with competitionMay 16 2019Slime mould plasmodia can adjust their behaviour in response to chemical trails left by themselves and other Physarum plasmodia. This simple feedback process increases their foraging efficiency. We still do not know whether other factors influence plasmodium ... More
The Energetics of Molecular Adaptation in Transcriptional RegulationMay 15 2019Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, ... More
Identifying conversion efficiency as a key mechanism underlying food webs evolution: A step forward, or backward?May 15 2019Body size or mass is generally seen as one of the main factors which structure food webs. A large number of evolutionary models have shown that indeed, the evolution of body size (or mass) can give rise to hierarchically organized trophic levels with ... More
Coevolutionary dynamics of a variant of the cyclic Lotka-Volterra model with three-agent interactionsMay 14 2019We study a variant of the cyclic Lotka-Volterra model with three-agent interactions. Inspired by a multiplayer variation of the Rock-Paper-Scissors game, the model describes an ideal ecosystem in which cyclic competition among three species develops through ... More
Aphids, Ants and Ladybirds: a mathematical model predicting their population dynamicsMay 13 2019The interaction between aphids, ants and ladybirds has been investigated from an ecological point of view since many decades, while there are no attempts to describe it from a mathematical point of view. This paper introduces a new mathematical model ... More
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer modelsMay 13 2019Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms, including - ... More
An Analysis of a Fishing Model with Nonlinear Harvesting FunctionMay 12 2019In this study, considering the importance of how to exploit renewable natural resources, we analyze a fishing model with nonlinear harvesting function in which the players at the equilibrium point do a static game with complete information that, according ... More
Alignment- and reference-free phylogenomics with colored de-Bruijn graphsMay 10 2019May 15 2019We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored ... More
Alignment- and reference-free phylogenomics with colored de-Bruijn graphsMay 10 2019We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored ... More