# Quantitative Biology - Populations and Evolution Publications (50)

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## Quantitative Biology - Populations and Evolution Publications

The most profound change in the relationship between humans and their environment was the introduction of agriculture and pastoralism. [.. Read More

Cancer is a disease of cellular regulation, often initiated by genetic mutation within cells, and leading to a heterogeneous cell population within tissues. In the competition for nutrients and growth space within the tumors the phenotype of each cell determines its success. Selection in this process is imposed by both the microenvironment (neighboring cells, extracellular matrix, and diffusing substances), and the whole of the organism through for example the blood supply. Read More

Whole genome duplication (WGD) is one of the most important events in the molecular evolution of organisms. In fish species, a WGD is considered to have occurred in the ancestral lineage of teleosts. Recent comprehensive ortholog comparisons among teleost genomes have provided useful data and insights into the fate of redundant genes generated by WGD. Read More

Zika virus (ZIKV) exhibits unique transmission dynamics in that it is concurrently spread by a mosquito vector and through sexual contact. We show that this sexual component of ZIKV transmission induces novel processes on networks through the highly asymmetric durations of infectiousness between males and females -- it is estimated that males are infectious for periods up to ten times longer than females -- leading to an asymmetric percolation process on the network of sexual contacts. We exactly solve the properties of this asymmetric percolation on random sexual contact networks and show that this process exhibits two epidemic transitions corresponding to a core-periphery structure. Read More

We investigate the effects of social interactions in task al- location using Evolutionary Game Theory (EGT). We propose a simple task-allocation game and study how different learning mechanisms can give rise to specialised and non- specialised colonies under different ecological conditions. By combining agent-based simulations and adaptive dynamics we show that social learning can result in colonies of generalists or specialists, depending on ecological parameters. Read More

Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set $X$ of taxa. This space, denoted $\mathcal{N}(X)$, is defined in terms of two operations on networks -- the nearest neighbor interchange and triangle operations -- which can be used to transform any network with leaf set $X$ into any other network with that leaf set. Read More

The stochastic dynamics of networks of biochemical reactions in living cells are typically modelled using chemical master equations (CMEs). The stationary distributions of CMEs are seldom solvable analytically, and few methods exist that yield numerical estimates with computable error bounds. Here, we present two such methods based on mathematical programming techniques. Read More

**Affiliations:**

^{1}MAMBA,

^{2}LJLL

We analyse the asymptotic behaviour of integro-differential equations modelling N populations in interaction, where interactions are modelled by non-local terms involving linear combinations of the total number of individuals in each population. This model generalises the usual Lotka-Volterra ordinary differential equations. Our aim is to give conditions under which there is global asymptotical stability of coexistence steady-states at the level of the total number of individuals in each species. Read More

We consider a class of birth-and-death processes describing a population made of sub-populations of $d$ different types which interact with one another. These processes are parametrized by a scaling parameter $K$ giving the order of magnitude of the total size of the population. We consider a situation where the process stabilizes during a very long time around a transient equilibrium close to the fixed point of a naturally associated dynamical system, before going almost surely to extinction. Read More

We study the population size time series of a Neotropical small mammal with the intent of detecting and modelling population regulation processes generated by density-dependent factors and their possible delayed effects. The application of analysis tools based on principles of statistical generality are nowadays a common practice for describing these phenomena, but, in general, they are more capable of generating clear diagnosis rather than granting valuable modelling. For this reason, in our approach, we detect the principal temporal structures on the bases of different correlation measures, and from these results we build an ad-hoc minimalist autoregressive model that incorporates the main drivers of the dynamics. Read More

We investigate theoretically if treatment alone can reduce the schistosomiasis's prevalence in an infected population, in a long-lasting sustainable way. We use a non-linear system of ordinary differential equations (a SI system combined with a logistic population growth) which describes the time evolution of the non-infected and infected populations, in terms of the recovering, infection, and demographic rates. Our model leads to the conclusion that the only way to eliminate this endemic disease is to implement public health policies aimed at both treatment and environment. Read More

This paper analyses an SIRS-type model for infectious diseases with account for behavioural changes associated with the simultaneous spread of awareness in the population. Two types of awareness are included into the model: private awareness associated with direct contacts between unaware and aware populations, and public information campaign. Stability analysis of different steady states in the model provides information about potential spread of disease in a population, and well as about how the disease dynamics is affected by the two types of awareness. Read More

A trademark of eusocial insect species is reproductive division of labor, in which workers forego their own reproduction while the queen produces almost all offspring. The presence of the queen is key for maintaining social harmony, but the specific role of the queen in the evolution of eusociality remains unclear. A long-discussed scenario is that a queen either behaviorally or chemically sterilizes her workers. Read More

Stochastic reaction-diffusion equations are a popular modelling approach for studying interacting populations in a heterogeneous environment under the influence of environmental fluctuations. Although the theoretical basis of alternative models such as Fokker-Planck diffusion is not less convincing, movement of populations is commonly modelled using the diffusion law due to Fick. It is an interesting feature of Fokker-Planck diffusion that for spatially varying diffusion coefficients the stationary solution is not a homogeneous distribution; in contrast to Fickian diffusion. Read More

We demonstrate the presence of chaos in stochastic simulations that are widely used to study biodiversity in nature. The investigation deals with a set of three distinct species that evolve according to the standard rules of mobility, reproduction and predation, with predation following the cyclic rules of the popular rock, paper and scissors game. The study uncovers the possibility to distinguish between time evolutions that start from slightly different initial states, guided by the Hamming distance which heuristically unveils the chaotic behavior. Read More

**Affiliations:**

^{1}Kansas

Recent 60Fe results have suggested that the estimated distances of supernovae in the last few million years should be reduced from 100 pc to 50 pc. Two events or series of events are suggested, one about 2.7 million years to 1. Read More

We consider a class of branching processes called Markovian binary trees, in which the individuals lifetime and reproduction epochs are modeled using a transient Markovian arrival process (TMAP). We estimate the parameters of the TMAP based on population data containing information on age-specific fertility and mortality rates. Depending on the degree of detail of the available data, a weighted non-linear regression method or a maximum likelihood method is applied. Read More

Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in the class of binary network. Read More

A key ecological parameter for planktonic copepods studies is their interspecies encounter rate which is driven by their behaviour and is strongly influenced by turbulence of the surrounding environment. A distinctive feature of copepods motility is their ability to perform quick displacements, often dubbed jumps, by means of powerful swimming strokes. Such a reaction has been associated to an escape behaviour from flow disturbances due to predators or other external dangers. Read More

We consider a fragmentation process that describes a specific way of successively removing objects from a linear arrangement. The process is a Markov chain, which is formulated in both a continuous-time and a discrete-time version. We aim at the law of the process over time. Read More

Since the late `60s, various genome evolutionary models have been proposed to predict the evolution of a DNA sequence as the generations pass. Most of these models are based on nucleotides evolution, so they use a mutation matrix of size 4x4. They encompass for instance the well-known models of Jukes and Cantor, Kimura, and Tamura. Read More

Vector-borne diseases with reservoir cycles are complex to understand because new infections come from contacts of the vector with humans and different reservoirs. In this scenario, the basic reproductive number $\mathcal{R}^h_0$ of the system where the reservoirs are not included could turn out to be less than one, yet, an endemic equilibrium be observed. Indeed, when the reservoirs are taken back into account, the basic reproductive number $\mathcal{R}_0^r$, of only vectors and reservoirs, explains the endemic state. Read More

Computer experiments, testing features proposed to explain the evolution of sexual recombination, show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor, rather than a simple transition from parthenogenesis to sexual recombination. Results show that sex is an adaptation to manage genetic complexity in evolution; that bisexual reproduction emerges only among anisogamic diploids with a synergistic division of reproductive labor; and that facultative sex is more likely to evolve among haploids practicing assortative mating. Looking at the evolution of sex as a complex system explains better the diversity of sexual strategies known to exist in nature. Read More

We define and examine a model of epidemic propagation for a virus such as Hepatitis C on a network of networks, namely the network of French urban areas. One network level is that of the individual interactions inside each urban area. The second level is that of the areas themselves, linked by individuals travelling between these areas and potentially helping the epidemic spread from one city to another. Read More

One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (MP). Read More

Regional tuna fishery management organizations cannot provide specific advice to local fishery managers in small island jurisdictions. The State of Hawaii maintains time series of yellowfin tuna catches dating back to 1949, but these data have never been formally applied to evaluating the effects of the yellowfin fishery in the Main Hawaiian Islands on the local stock. I develop a new approach utilizing these data that links the local stock dynamics to the dynamics of the larger Pacific stock. Read More

We study a stochastic model of infection spreading on a network. At each time step a node is chosen at random, along with one of its neighbors. If the node is infected and the neighbor is susceptible, the neighbor becomes infected. Read More

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability relies on the existence of sufficiently large genotype networks, that is ensembles of sequences with the same phenotype that guarantee an efficient random drift through sequence space. The number of sequences compatible with a given structure (e. Read More

Many biological populations, such as bacterial colonies, have developed through evolution a protection mechanism, called bet-hedging, to increase their probability of survival under stressful environmental fluctutation. In this context, the concept of preadaptation refers to a common type of bet-hedging protection strategy in which a relatively small number of individuals in a population stochastically switch their phenotypes to a `dormant' metabolic state in which they increase their probability of survival against potential environmental shocks. Hence, if an environmental shock took place at some point in time, preadapted organisms would be better adapted to survive and proliferate once the shock is over. Read More

In this paper, we show that many structured epidemic models may be described using a straightforward product structure. Such products, derived from products of directed graphs, may represent useful refinements including geographic and demographic structure, age structure, gender, risk groups, or immunity status. Extension to multi-strain dynamics, i. Read More

We introduce a new tuberculosis (TB) mathematical model, with $25$ state-space variables where $15$ are evolution disease states (EDSs), which generalises previous models and takes into account the (seasonal) flux of populations between a high incidence TB country (A) and a host country (B) with low TB incidence, where (B) is divided into a community (G) with high percentage of people from (A) plus the rest of the population (C). Contrary to some beliefs, related to the fact that agglomerations of individuals increase proportionally to the disease spread, analysis of the model shows that the existence of semi-closed communities are beneficial for the TB control from a global viewpoint. The model and techniques proposed are applied to a case-study with concrete parameters, which model the situation of Angola (A) and Portugal (B), in order to show its relevance and meaningfulness. Read More

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph having a unique root in which the leaves are labelled by a given set of species. Recently, some approaches have been developed to construct phylogenetic networks from collections of networks on 2- and 3-leaved networks, which are known as binets and trinets, respectively. Read More

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$ (for example, an evolutionary tree), which is usually also binary, i.e. Read More

Positive density-dependence occurs when individuals experience increased survivorship, growth, or reproduction with increased population densities. Mechanisms leading to these positive relationships include mate limitation, saturating predation risk, and cooperative breeding and foraging. Individuals within these populations may differ in age, size, or geographic location and thereby structure these populations. Read More

Salmon farming has become a prosperous international industry over the last decades. Along with growth in the production farmed salmon, however, an increasing threat by pathogens has emerged. Of special concern is the propagation and spread of the salmon louse, Lepeophtheirus salmonis. Read More

We study macroevolutionary dynamics by extending microevolutionary competition models to long time scales. It has been shown that for a general class of competition models, gradual evolutionary change in continuous phenotypes (evolutionary dynamics) can be non-stationary and even chaotic when the dimension of the phenotype space in which the evolutionary dynamics unfold is high. It has also been shown that evolutionary diversification can occur along non-equilibrium trajectories in phenotype space. Read More

We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct a hypothesis test between these two model classes. The null and alternative sampling distributions of our statistic are intractable, but its low dimensionality renders these distributions amenable to Monte Carlo estimation. We construct kernel density estimates of the sampling distributions based on simulated data, and show that the resulting hypothesis test dramatically improves on the statistical power of a current state-of-the-art method. Read More

We deal with the study of the evolution of the allelic frequencies, at a single locus, for a population distributed continuously over a bounded habitat. We consider evolution which occurs under the joint action of selection and arbitrary migration, that is independent of genotype, in absence of mutation and random drift. The focus is on a conjecture, that was raised up in literature of population genetics, about the possible uniqueness of polymorphic equilibria, which are known as clines, under particular circumstances. Read More

Evolutionary event relations such as orthology, paralogy and xenology provide important information on the evolutionary history of the investigated genes. It has recently been shown that there is an event-labeled gene tree that displays estimated event relations if and only if the (graph-representation of these) relations are so-called cographs, resp., uniformly non-prime 2-structures. Read More

Social conventions govern countless behaviors all of us engage in every day, from how we greet each other to the languages we speak. But how can shared conventions emerge spontaneously in the absence of a central coordinating authority? The Naming Game model shows that networks of locally interacting individuals can spontaneously self-organize to produce global coordination. Here, we provide a gentle introduction to the main features of the model, from the dynamics observed in homogeneously mixing populations to the role played by more complex social networks, and to how slight modifications of the basic interaction rules give origin to a richer phenomenology in which more conventions can co-exist indefinitely. Read More

Coalescent models of evolution account for incomplete lineage sorting by specifying a species tree parameter which determines a distribution on gene trees. It has been shown that the unrooted topology of the species tree parameter of the multispecies coalescent is generically identifiable. Moreover, a statistically consistent reconstruction method called SVDQuartets has been developed to recover this parameter. Read More

While interdependent systems have usually been associated with increased fragility, we show that strengthening the interdependence between dynamical processes on different networks can make them more robust. By coupling the dynamics of networks that in isolation exhibit catastrophic collapse with extinction of nodal activity, we demonstrate system-wide persistence of activity for an optimal range of interdependence between the networks. This is related to the appearance of attractors of the global dynamics comprising disjoint sets ("islands") of stable activity. Read More

Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection by increasing or decreasing the fixation probability of a beneficial mutant. Properties of the associated mean fixation times can be more intricate, especially when selection is strong. Read More

An ecosystem made of nutrients, plants, detritus and dissolved oxygen is presented. Its equilibria are established. Sufficient conditions for the existence of the coexistence equilibrium are derived and its feasibility is discussed in every detail. Read More

In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two directions. We show that for any tree $T$ there exists a family of non-trivial HGT networks $N$ for which the distance metric $d_N$ affords a metric on $T$. Read More

Despite recent advances in reputation technologies, it is not clear how reputation systems can affect human cooperation in social networks. Although it is known that two of the major mechanisms in the evolution of cooperation are spatial selection and reputation-based reciprocity, theoretical study of the interplay between both mechanisms remains almost uncharted. Here, we present a new individual-based model for the evolution of reciprocal cooperation between reputation and networks. Read More

Since penicillin was discovered about 90 years ago, we have become used to using drugs to eradicate unwanted pathogenic cells. However, using drugs to kill bacteria, viruses or cancer cells has the serious side effect of selecting for mutant types that survive the drug attack. A key question therefore is how one could kill as many cells as possible for a given acceptable risk of drug resistance evolution. Read More

We re-examined data from the classic Luria-Delbruck fluctuation experiment, which is often credited with establishing a Darwinian basis for evolution. We argue that, for the Lamarckian model of evolution to be ruled out by the experiment, the experiment must favor pure Darwinian evolution over both the Lamarckian model and a model that allows both Darwinian and Lamarckian mechanisms. Analysis of the combined model was not performed in the original 1943 paper. Read More

Dengue fever is increasing in geographical range, spread by invasion of its vector mosquitoes. The trade in second-hand tires has been implicated as a factor in this process as they act as mobile reservoirs of mosquito eggs and larvae. Regional transportation of tires can create linkages between rural areas with dengue to disease-free urban areas, potentially giving rise to outbreaks even in areas with strong local control measures. Read More