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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 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
Gender differences in the equity-efficiency trade-offMay 10 2019Gender differences in human behaviour have attracted generations of social scientists, who have explored whether males and females act differently in domains involving competition, risk taking, cooperation, altruism, honesty, as well as many others. Yet, ... More
When Can The Discrete Moran Process May Bereplaced By Wright-fisher Diffusion?May 10 2019The Moran discrete process and the Wright-Fisher modelare the most popular models in population genetics. It is common tounderstand the dynamics of these models to use an approximating diffusionprocess, called Wright-Fisher diffusion. Here, we give a ... More
Stable cycling in quasi-linkage equilibrium: fluctuating dynamics under gene conversion and selectionMay 09 2019Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of recognition-dependent ... More
Species diversity in a metacommunity with patches connected by periodic coalescence: a neutral modelMay 09 2019The recent realization that entire communities fuse and separate (community coalescence) has led to a reappraisal of the forces determining species diversity and dynamics, especially in microbial communities where coalescence is likely widespread. To ... More
Death by starvation in May-Leonard modelsMay 08 2019We consider the dynamics of spatial stochastic May-Leonard models with mutual predation interactions of equal strength between any two individuals of different species. Using two-dimensional simulations, with two and three pecies, we investigate the dynamical ... More
On age-specific selection and extensive lifespan beyond menopauseMay 08 2019Extensive post reproductive lifespan (PRLS) is observed only in a few species, such as humans or resident killer whales, and its origin is under debate. Hypotheses like mother-care and grandmother-care invoke strategies of investment--provision to one's ... More
Invasion controlled pattern formation in a generalized multi-species predator-prey systemMay 07 2019Rock-scissors-paper game, as the simplest model of intransitive relation between competing agents, is a frequently quoted model to explain the stable diversity of competitors in the race of surviving. When increasing the number of competitors we may face ... More
Mathematical analysis of an extended cellular model of the Hepatitis C Virus infection with non-cytolytic processMay 07 2019The aims of this work is to analyse of the global stability of the extended model of hepatitis C virus(HCV) infection with cellular proliferation, spontaneous cure and hepatocyte homeostasis. We first give general information about hepatitis C. Secondly, ... More
Applying allometric scaling to predator-prey systemsMay 07 2019In population dynamics, mathematical models often contain too many parameters to be easily testable. A way to reliably estimate parameters for a broad range of systems would help us obtain clearer predictions from theory. In this paper, we examine how ... More
Bayesian modeling of two-species bacterial competition growth and decline rates in milkMay 07 2019Shiga toxin-producing Escherichia coli O157: H7 is a food-borne pathogen and the major cause of hemorrhagic colitis. Pseudomonas is the genus most frequent psychrotrophic spoilage microorganisms present in milk. Two-species bacterial systems with Escherichia ... More
Tree-based Reconstruction of Ecological Network from Abundance DataMay 07 2019The behavior of ecological systems mainly relies on the interactions between the species it involves. In many situations, these interactions are not observed and have to be inferred from species abundance data. To be relevant, any reconstruction network ... More
The effect of intermittent upwelling events on plankton bloomsMay 06 2019In the marine environment biological processes are strongly affected by oceanic currents, particularly by eddies (vortices) formed by the hydrodynamic flow field. Employing a kinematic flow field coupled to a population dynamical model for plankton growth, ... More
Maximum likelihood (ML) estimators for scaled mutation parameters with a strand symmetric mutation model in equilibriumMay 06 2019With the multiallelic parent-independent mutation-drift model, the equilibrium proportions of alleles are known to be Dirichlet distributed. A special case is the biallelic model, in which the proportions are beta distributed. A sample taken from these ... More
Development of a Forecasting and Warning System on the Ecological Life-Cycle of Sunn PestMay 05 2019We provide a machine learning solution that replaces the traditional methods for deciding the pesticide application time of Sunn Pest. We correlate climate data with phases of Sunn Pest in its life-cycle and decide whether the fields should be sprayed. ... More
Scaling of the risk landscape drives optimal life history strategies and the evolution of grazingMay 04 2019Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure ... More
Evolving generalists via dynamic sculpting of rugged landscapesMay 04 2019Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to genotypes ... More
New reduction rules for the tree bisection and reconnection distanceMay 04 2019Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k-9 taxa where k is the TBR (Tree Bisection and Reconnection) distance between ... More
A Two-Dose Vaccine Epidemic Model with Power Incidence RateMay 02 2019The dynamics of a SIVR model with power relationship incidence rates $(\beta I^p S^q)$ is investigated. It is assumed an individual can be susceptible after receiving the first dose of the vaccine, hence a second dose is required to attain permanent immunity. ... More
A hierarchical life cycle model for Atlantic salmon stock assessment at the North Atlantic basin scaleMay 02 2019We developed an integrated hierarchical Bayesian life cycle model that simultaneously estimates the abundance of post-smolts at sea, post-smolt survival rates, and proportions maturing as 1SW, for all SU in Northern Europe, Southern Europe and North America. ... More
Modeling the ASF (African Swine Fever) spread till summer 2017 and risk assessment for PolandMay 02 2019African Swine Fever (ASF) is viral infection which causes acute disease in domestic pigs and wild boar. Although the virus does not cause disease in humans, the impact it has on the economy, especially through trade and farming, is substantial. Recent ... More
Homogeneous and Heterogeneous Response of Quorum-Sensing Bacteria in an Evolutionary ContextMay 01 2019To explain the stability of cooperation is a central task of evolutionary theory. We investigate this question in the case of quorum sensing (QS) bacteria, which regulate cooperative traits in response to population density. Cooperation is modeled by ... More
The effects of imitation dynamics on vaccination behaviors in SIR-network modelMay 01 2019We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures ... More
The effects of imitation dynamics on vaccination behaviours in SIR-network modelMay 01 2019May 13 2019We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures ... More
The effects of imitation dynamics on vaccination behaviours in SIR-network modelMay 01 2019May 08 2019We present a series of SIR-network models, extended with a game-theoretic treatment of imitation dynamics which result from regular population mobility across residential and work areas and the ensuing interactions. Each considered SIR-network model captures ... More
Epidemics on Networks: Reducing Disease Transmission Using Health Emergency Declarations and Peer CommunicationApr 29 2019Understanding individual decisions in a world where communications and information move instantly via cell phones and the internet, contributes to the development and implementation of policies aimed at stopping or ameliorating the spread of diseases. ... More
Epistasis between cultural traits drives paradigm shifts in cultural evolutionApr 29 2019Every now and then the cultural paradigm of a society changes. Human history can be regarded as a sequence of long periods of cultural stasis punctuated by paradigm shifts that transform culture upside-down over the turn of a few generations. We propose ... More
Predictive Situation Awareness for Ebola Virus Disease using a Collective Intelligence Multi-Model Integration Platform: Bayes CloudApr 29 2019May 04 2019The humanity has been facing a plethora of challenges associated with infectious diseases, which kill more than 6 million people a year. Although continuous efforts have been applied to relieve the potential damages from such misfortunate events, it is ... More
Predictive Situation Awareness for Ebola Virus Disease using a Collective Intelligence Multi-Model Integration Platform: Bayes CloudApr 29 2019The humanity has been facing a plethora of challenges associated with infectious diseases, which kill more than 6 million people a year. Although continuous efforts have been applied to relieve the potential damages from such misfortunate events, it is ... More
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patternsApr 29 2019Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify ... More
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patternsApr 29 2019May 03 2019Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify ... More
Ranking top-k trees in tree-based phylogenetic networksApr 29 2019'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support trees', about ... More
A time-fractional Lotka-Volterra model with mutualistic predationApr 28 2019In this work, we present a predator-prey type model where the two predator species engage in mutualistic predation. Constant effort harvesting is also incorporated. Linear stability analysis of the resulting models is performed and it is shown that harvesting ... More
Best Match Graphs and Reconciliation of Gene Trees with Species TreesApr 26 2019A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify ... More
Best Match Graphs and Reconciliation of Gene Trees with Species TreesApr 26 2019May 15 2019A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify ... More
Evolutionary dynamics of group cooperation with asymmetrical environmental feedbackApr 24 2019In recent years, there has been growing interest in studying evolutionary games with environmental feedback. Previous studies exclusively focus on two-player games. However, extension to multi-player game is needed to study problems such as microbial ... More
How self-regulation, the storage effect and their interaction contribute to coexistence in stochastic and seasonal environmentsApr 24 2019Explaining coexistence in species-rich communities of primary producers remains a challenge for ecologists because of their likely competition for shared resources. Following Hutchinson's seminal suggestion, many theoreticians have tried to create diversity ... More
Coalescence in the diffusion limit of a Bienayme-Galton-Watson branching processApr 24 2019We consider the problem of estimating the elapsed time since the most recent common ancestor of a finite random sample drawn from a population which has evolved through a Bienayme-Galton-Watson branching process. More specifically, we are interested in ... More
Relation of the Weibull Shape Parameter with the Healthy Life Years Lost Estimates: Analytic Derivation and Estimation from an Extended Life TableApr 23 2019Matsushita et al (1992) have done an interesting finding. They observed that the shape parameter of the Weibull model presented systematic changes over time and age when applied to mortality data for males and females in Japan. They have also estimated ... More
Spatial Population Genetics: It's About TimeApr 22 2019Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where? How do they move and interbreed across the landscape? How were they moving a thousand years ago, and where did the ancestors ... More
Spatial Population Genetics: It's About TimeApr 22 2019May 10 2019Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years ago, and where ... More
On equilibrium properties of the mutator-replicator equation in deterministic and random gamesApr 22 2019In this paper, we study the number of equilibria of the replicator-mutator dynamics for both deterministic and random multi-player two-strategy evolutionary games. For deterministic games, using Decartes' rule of signs, we provide a formula to compute ... More
Linear Stability Invariant Metapopulations Network PartitioningApr 22 2019Metapopulations is a multi-patch habitat system, where populations live and interact in habitat patches, and individuals disperse from one patch to other via dispersal connections. The loss of dispersal connections among habitat patches can impact negatively ... More
Extremal properties of the Colless balance index for rooted binary treesApr 22 2019Measures of tree balance play an important role in various research areas, for example in phylogenetics. There they are for instance used to test whether an observed phylogenetic tree differs significantly from a tree generated by the Yule model of speciation. ... More
The Community Simulator: A Python package for microbial ecologyApr 19 2019Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available ... More
The Effect of Recombination on the Speed of EvolutionApr 18 2019It has been a puzzling question why some organisms reproduce sexually. Fisher and Muller hypothesized that reproducing by sex can speed up the evolution. They explained that in the sexual reproduction, recombination can combine beneficial alleles that ... More
A trio of heteroclinic bifurcations arising from a model of spatially-extended Rock-Paper-ScissorsApr 18 2019One of the simplest examples of a robust heteroclinic cycle involves three saddle equilibria: each one is unstable to the next in turn, and connections from one to the next occur within invariant subspaces. Such a situation can be described by a third-order ... More
A Multi-agent approach for $\textit{in silico}$ simulations of micro-biological systemsApr 16 2019Using a Multi-agent systems paradigm, the present project develops, validates and exploits a computational $\textit{testbed}$ that simulates micro-biological complex systems, namely the aggregation patterns of the social amoeba $\textit{Dyctiostelium ... More
On non-negative solutions to large systems of random linear equationsApr 15 2019Systems of random linear equations may or may not have solutions with all components being non-negative. The question is, e.g., of relevance when the unknowns are concentrations or population sizes. In the present paper we show that if such systems are ... More
Uneven rock-paper-scissors models: patterns and coexistenceApr 15 2019We study a class of the stochastic May-Leonard models, with three species dominating each other in a cyclic nonhierarchical way, according to the rock-paper-scissors game. We introduce an unevenness in the system, by considering that one the species is ... More
Uneven rock-paper-scissors models: patterns and coexistenceApr 15 2019May 14 2019We study a class of the stochastic May-Leonard models, with three species dominating each other in a cyclic nonhierarchical way, according to the rock-paper-scissors game. We introduce an unevenness in the system, by considering that one of the species ... More
Resilience for stochastic systems interacting via a quasi-degenerate networkApr 14 2019A stochastic reaction-diffusion model is studied on a networked support. In each patch of the network two species are assumed to interact following a non-normal reaction scheme. When the interaction unit is replicated on a directed linear lattice, noise ... More
Are the better cooperators dormant or quiescent?Apr 14 2019Despite the wealth of empirical and theoretical studies, the origin and maintenance of cooperation is still an evolutionary riddle. In this context, ecological life-history traits which affect the efficiency of selection may play a role, though these ... More
On the effect of forcing of fold bifurcations and early-warning signals in population dynamicsApr 13 2019The classical fold bifurcation is a paradigmatic example of a critical transition. It has been used in a variety of contexts, including in particular ecology and climate science, to motivate the role of slow recovery rates and increased autocorrela tions ... More
A mean first passage time genome rearrangement distanceApr 12 2019This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from control theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the theory and introduce ... More
A tale of two species: How humans shape dog behaviour in urban habitatsApr 12 2019Species inhabiting urban environments experience enormous anthropogenic stress. Behavioural plasticity and flexibility of temperament are crucial to successful urban-adaptation. Urban free-ranging dogs experience variable human impact, from positive to ... More
Understanding Adaptive Immune System as Reinforcement LearningApr 11 2019The adaptive immune system can detect, respond to, and learn diverse pathogens from the past experience. While the clonal selection of the T helper (Th) cells is the simple and established mechanism for learning a better recognition of new pathogens, ... More
Predicting Earth's Carrying Capability of Human Population as the Predator and the Natural Resources as the Prey in the Modified Lokta-Volterra Equations with Time-dependent ParametersApr 10 2019We modified the Lotka-Volterra Equations with the assumption that two of the original four constant parameters in the traditional equations are time dependent. In the first place, we assumed that the human population (borrowed from the T-Function) plays ... More
Nowcasting Influenza Incidence with CDC Web Traffic Data: A Demonstration Using a Novel Data SetApr 09 2019Influenza epidemics result in a public health and economic burden around the globe. Traditional surveillance techniques, which rely on doctor visits, provide data with a delay of 1-2 weeks. A means of obtaining real-time data and forecasting future outbreaks ... More
Identification of similarity amongst eucalyptus planted areas based on leaf-cutting ant nest sizesApr 09 2019Techniques for leaf-cutting ant control have been investigated in literature due to the importance of the damage they cause to agriculture. The effectiveness of different forms of control is explored in researches aimed at identifying the balance between ... More
Identification of similarity amongst eucalyptus planted areas based on leaf-cutting ant nest sizesApr 09 2019Apr 16 2019Techniques for leaf-cutting ant control have been investigated in literature due to the importance of the damage they cause to agriculture. The effectiveness of different forms of control is explored in researches aimed at identifying the balance between ... More
Single-species fragmentation: the role of density-dependent feedbacksApr 08 2019Internal feedbacks are commonly present in biological populations and can play a crucial role in the emergence of collective behavior. We consider a generalization of Fisher-KPP equation to describe the temporal evolution of the distribution of a single-species ... More
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoiresApr 08 2019The adaptive immune system is a natural diagnostic and therapeutic. It recognizes threats earlier than clinical symptoms manifest and neutralizes antigen with exquisite specificity. Recognition specificity and broad reactivity is enabled via adaptive ... More
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoiresApr 08 2019Apr 09 2019The adaptive immune system is a natural diagnostic and therapeutic. It recognizes threats earlier than clinical symptoms manifest and neutralizes antigen with exquisite specificity. Recognition specificity and broad reactivity is enabled via adaptive ... More
Species Tree Estimation Using ASTRAL: Practical ConsiderationsApr 08 2019ASTRAL is a method for reconstructing species trees after inferring a set of gene trees and is increasingly used in phylogenomic analyses. It is statistically consistent under the multi-species coalescent model, is scalable, and has shown high accuracy ... More
Trivial pursuitsApr 07 2019We demonstrate that the conclusions drawn by Bernhard et al. (2018) regarding the ability of nonlinear averaging to accurately predict organismal performance under fluctuating temperatures are flawed because of a series of experimental and statistical ... More
The role of dose-density in combination cancer chemotherapyApr 06 2019A multicompartment mathematical model is presented with the goal of studying the role of dose-dense protocols in the context of combination cancer chemotherapy. Dose-dense protocols aim at reducing the period between courses of chemotherapy from three ... More
Dynamics of a combinatorial birth-death process based on the 'adjacent possible'Apr 05 2019A feature of human creativity is the ability to take a subset of existing items (e.g. objects, ideas, or techniques) and combine them in various ways to give rise to new items, which, in turn, fuel further growth. Occasionally, some of these items may ... More
Transmission of danger information past physical barriers by antsApr 05 2019Can insects transmit information about a threat through a physical barrier they cannot cross? While the emission and detection of alarm pheromones is the universally accepted mechanism of panic communication, there are still open questions about the specific ... More
Cell damage and mitigation in Swiss albino mice: experiment and modellingApr 05 2019Chronic exposure to inorganic arsenic is a potential cause of carcinogenesis. It elicits its potential by generation of ROS, leading to DNA, protein and lipid damage. Therefore, the deleterious effect of arsenic can be mitigated by quenching ROS using ... More
Large-scale Species Tree EstimationApr 04 2019Apr 06 2019Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called deep coalescence), ... More
Large-scale Species Tree EstimationApr 04 2019Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called deep coalescence), ... More
Fitting stochastic predator-prey models using both population density and kill rate dataApr 03 2019Most mechanistic predator-prey modelling has involved either parameterization from process rate data or inverse modelling. Here, we take a median road: we aim at identifying the potential benefits of combining datasets, when both population growth and ... More
No evidence of fish biodiversity effects on coral reef ecosystem functioning across scalesApr 03 2019We demonstrate that the conclusions drawn by Lefcheck et al. (2019) regarding the positive effects of fish diversity on coral reef ecosystem functioning across scales are flawed because of a series of conceptual and statistical issues that include spurious ... More
No evidence of fish biodiversity effects on coral reef ecosystem functioning across scalesApr 03 2019Apr 07 2019We demonstrate that the conclusions drawn by Lefcheck et al. (2019) regarding the positive effects of fish diversity on coral reef ecosystem functioning across scales are flawed because of a series of conceptual and statistical issues that include spurious ... More
Strategies that enforce linear payoff relationships under observation errors in Repeated Prisoner's Dilemma gameApr 02 2019The theory of repeated games analyzes the long-term relationship of interacting players and mathematically reveals the condition of how cooperation is achieved, which is not achieved in a one-shot game. In the repeated prisoner's dilemma (RPD) game with ... More
Diverse communities behave like typical random ecosystemsApr 01 2019With a brief letter to Nature in 1972, Robert May triggered a worldwide research program in theoretical ecology and complex systems that continues to this day. Building on powerful mathematical results about large random matrices, he argued that systems ... More
Far-ranging generalist top predators enhance the stability of meta-foodwebsApr 01 2019Identifying stabilizing factors in foodwebs is a long standing challenge with wide implications for community ecology and conservation. Here, we investigate the stability of spatially resolved meta-foodwebs with far-ranging super-predators for whom the ... More
Serostatus Testing & Dengue Vaccine Cost-Benefit ThresholdsMar 30 2019The World Health Organisation currently recommends pre-screening for past infection prior to administration of the only licensed dengue vaccine, CYD-TDV. Using a bounding analysis, we show that despite additional testing costs, this approach can improve ... More
Simple unity among the fundamental equations of scienceMar 29 2019The Price equation describes the change in populations. Change concerns some value, such as biological fitness, information or physical work. The Price equation reveals universal aspects for the nature of change, independently of the meaning ascribed ... More
Accessibility percolation in random fitness landscapesMar 28 2019The fitness landscape encodes the mapping of genotypes to fitness and provides a succinct representation of possible trajectories followed by an evolving population. Evolutionary accessibility is quantified by the existence of fitness-monotonic paths ... More
Estimating effective population size changes from preferentially sampled genetic sequencesMar 28 2019Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through time and the distribution ... More
The minimum value of the Colless indexMar 27 2019May 07 2019The Colless index is one of the oldest and most widely used balance indices for rooted bifurcating trees. Despite its popularity, its minimum value on the space $\mathcal{T}_n$ of rooted bifurcating trees with $n$ leaves is only known when $n$ is a power ... More
The minimum value of the Colless indexMar 27 2019The Colless index is one of the oldest and most widely used balance indices for rooted bifurcating trees. Despite its popularity, its minimum value on the space $\mathcal{T}_n$ of rooted bifurcating trees with $n$ leaves is only known when $n$ is a power ... More
The minimum value of the Colless indexMar 27 2019Apr 08 2019The Colless index is one of the oldest and most widely used balance indices for rooted bifurcating trees. Despite its popularity, its minimum value on the space $\mathcal{T}_n$ of rooted bifurcating trees with $n$ leaves is only known when $n$ is a power ... More
Genetic drift in range expansions is very sensitive to density feedback in dispersal and growthMar 27 2019Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants ... More
Modelling the impact of deep-water crustacean trawl fishery in the marine ecosystem off Portuguese Southwestern and South Coasts: I) the trophic web and trophic flowsMar 27 2019The concentration of the population in coastal regions, in addition to the direct human use, is leading to an accelerated process of change and deterioration of the marine ecosystems. Human activities such as fishing together with environmental drivers ... More
A general mathematical framework for understanding the behavior of heterogeneous stem cell regenerationMar 27 2019Stem cell heterogeneity is essential for the homeostasis in tissue development. This paper established a general formulation for understanding the dynamics of stem cell regeneration with cell heterogeneity and random transitions of epigenetic states. ... More
Dynamic Control of Stochastic Evolution: A Deep Reinforcement Learning Approach to Adaptively Targeting Emergent Drug ResistanceMar 27 2019The challenge in controlling stochastic systems in which random events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of the baseline control policy. ... More
Why understanding multiplex social network structuring processes will help us better understand the evolution of human behaviorMar 26 2019Anthropologists have long appreciated that single-layer networks are insufficient descriptions of human interactions---individuals are embedded in complex networks with dependencies. One debate explicitly about this surrounds food sharing. Some argue ... More
Cross-scale cooperation enables sustainable use of a common-pool resourceMar 26 2019In social-ecological systems (SESs), social and biophysical dynamics interact within and between structural levels separated by spatial and temporal scales. Cross-scale interactions (CSIs) are interdependences between processes at different scales, generating ... More