Quantitative Biology - Populations and Evolution Publications (50)

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Quantitative Biology - Populations and Evolution Publications

In this work we study the limit distribution of an appropriately normalized cophenetic index of the pure birth tree on n contemporary tips. We show that this normalized phylogenetic balance index is a submartingale that converges almost surely and in L2. We link our work with studies on trees without branch lengths and show that in this case the limit distribution is a contraction type distribution, similar to the Quicksort limit distribution. Read More


The dynamics of a mosquito population depends heavily on climatic variables such as temperature and precipitation. Since climate change models predict that global warming will impact on the frequency and intensity of rainfall, it is important to understand how these variables affect the mosquito populations. We present a model of the dynamics of a {\it Culex quinquefasciatus} mosquito population that incorporates the effect of rainfall and use it to study the influence of the number of rainy days and the mean monthly precipitation on the maximum yearly abundance of mosquitoes $M_{max}$. Read More


We introduce a new dominance concept consisting of three new dominance metrics based on Lloyd's (1967) mean crowding index. The new metrics link communities and species, whereas existing ones are applicable only to communities. Our community-level metric is a function of Simpson's diversity index. Read More


We study a birth and death model for the adapatation of a sexual population to an environment. The population is structured by a phenotypical trait, and, possibly, an age variable. Recombination is modeled by Fisher's infinitesimal operator. Read More


A six year field study was conducted from 2001 2002 to 2006 2007 at Punjab Agricultural University, Ludhiana, India to study the losses in seed yield of different Brassica species (B. juncea, B. napus, B. Read More


The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associated hierarchical web of species interdependence. We report a large scale study of microbial diversity that reveals that the cumulative number of genes discovered increases with the number of genomes studied as a simple power law. Read More


Infectious disease outbreaks recapitulate biology: they emerge from the multi-level interaction of hosts, pathogens, and their shared environment. As a result, predicting when, where, and how far diseases will spread requires a complex systems approach to modeling. Recent studies have demonstrated that predicting different components of outbreaks--e. Read More


Consumer demand for plant and animal products threatens many populations with extinction. The anthropogenic Allee effect (AAE) proposes that such extinctions can be caused by prices for wildlife products increasing with species rarity. This price-rarity relationship creates financial incentives to extract the last remaining individuals of a population, despite higher search and harvest costs. Read More


Pre-exposure prophylaxis (PrEP) consists in the use of an antiretroviral medication to prevent the acquisition of HIV infection by uninfected individuals and has recently demonstrated to be highly efficacious for HIV prevention. We propose a new epidemiological model for HIV/AIDS transmission including PrEP. Existence, uniqueness and global stability of the disease free and endemic equilibriums are proved. Read More


Relations among species in ecosystems can be represented by complex networks where both negative (competition) and positive (mutualism) interactions are concurrently present. Recently, it has been shown that many ecosystems can be cast into mutualistic networks, and that nestedness reduces effective inter-species competition, thus facilitating mutually beneficial interactions and increasing the number of coexisting species or the biodiversity. However, current approaches neglect the structure of inter-species competition by adopting a mean-field perspective that does not deal with competitive interactions properly. Read More


We develop a simple mechanism of anonymous network interactions identified as a form of generalized reciprocity - a concept organized around the premise "help anyone if helped by someone". The mechanism protects nodes from exploitation by other nodes, in contrast to other mechanisms based on generalized reciprocity which leave the nodes vulnerable to exploitation due to anonymity of donors and receivers. We demonstrate that the network propensity for cooperation is determined by a network centrality measure here referred to as neighborhood importance index. Read More


The fact that Parsimony may fail is not new. However, here we proved that no mater of what topology the true 9-taxon and greater species tree is the only thing you need to fail Parsimony is to have in this tree three consecutive edges with lengths of some proportions. Obviously, the probability to meet these lengths is growing in general with the size of species tree. Read More


We study a model of seed dispersal that consists of an animal moving diffusively, feeding on fruits and dispersing the seeds, which are later deposited and capable of germination. The dynamics depends on several population parameters of growth, decay, harvesting, transport, digestion and germination. In particular, the deposition of transported seeds at places away from their collection sites produces a delay in the dynamics, whose effects are the focus of this work. Read More


Chemotherapy is a class of cancer treatment that uses drugs to kill cancer cells. A typical chemotherapeutic protocol consists of several drugs delivered in cycles of three weeks. We present mathematical analyses demonstrating the existence of a minimum time between cycles of chemotherapy for a protocol to be effective. Read More


Finding influential spreaders of information and disease in networks is an important theoretical problem, and one of considerable recent interest. It has been almost exclusively formulated as a node-ranking problem -- methods for identifying influential spreaders rank nodes according to how influential they are. In this work, we show that the ranking approach does not necessarily work: the set of most influential nodes depends on the number of nodes in the set. Read More


We investigate the formation of stable ecological networks where many species share the same resource. We show that such stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of coexisting species and find a relation describing how many species that may go extinct as a result of a sharp environmental change. Read More


We consider a recent coinfection model for Tuberculosis (TB), Human Immunodeficiency Virus (HIV) infection and Acquired Immunodeficiency Syndrome (AIDS) proposed in [Discrete Contin. Dyn. Syst. Read More


Variations in mitochondrial genes are usually considered to infer phylogenies. However some of these genes are lesser constraint than other ones, and thus may blur the phylogenetic signals shared by the majority of the mitochondrial DNA sequences. To investigate such effects, in this research work, the molecular phylogeny of the genus Taenia is studied using 14 coding sequences extracted from mitochondrial genomes of 17 species. Read More


In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have efficiently computable metrics with which to systematically compare such networks. Through developing an optimal algorithm to enumerate all trinets displayed by a level-1 network (a type of network that is slightly more general than an evolutionary tree), here we propose a cubic-time algorithm to compute the trinet distance between two level-1 networks. Read More


Avalanches of electrochemical activity in brain networks have been empirically reported to obey scale-invariant behavior --characterized by power-law distributions up to some upper cut-off-- both in vitro and in vivo. Elucidating whether such scaling laws stem from the underlying neural dynamics operating at the edge of a phase transition is a fascinating possibility, as systems poised at criticality have been argued to exhibit a number of important functional advantages. Here we employ a well-known model for neural dynamics with synaptic plasticity, to elucidate an alternative scenario in which neuronal avalanches can coexist, overlapping in time, but still remaining scale-free. Read More


We present an analysis of an avian flu model that yields insight into the role of different transmission routes in the recurrence of avian influenza epidemics. Recent modelling work on avian influenza in wild bird populations takes into account demographic stochasticity and highlights the importance of environmental transmission in determining the outbreak periodicity, but only for a weak between-host transmission rate. We determine the relative contribution of environmental and direct transmission routes to the intensity of outbreaks. Read More


We study the persistence and extinction of species in a simple food chain that is modelled by a Lotka-Volterra system with environmental stochasticity. There exist sharp results for deterministic Lotka-Volterra systems in the literature but few for their stochastic counterparts. The food chain we analyze consists of one prey and $n-1$ predators. Read More


Uncovering the mechanisms that control size, growth, and division rates of systems reproducing through binary division means understanding basic principles of their life cycle. Recent work has focused on how division rates are regulated in bacteria and yeast, but this question has not yet been addressed in more complex, multicellular organisms. We have acquired a unique large-scale data set on the growth and asexual reproduction of two freshwater planarian species, Dugesia japonica and Dugesia tigrina, which reproduce by transverse fission and succeeding regeneration of head and tail pieces into new planarians. Read More


Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be grouped together. However, it has long been known that some characters contain more information than others. Read More


Variation in behavior among group members often impacts collective outcomes. Individuals may vary both in the task that they perform and in the persistence with which they perform each task. Although both the distribution of individuals among tasks and differences among individuals in behavioral persistence can each impact collective behavior, we do not know if and how they jointly affect collective outcomes. Read More


We develop a multi-patch and multi-group model that captures the dynamics of an infectious disease when the host is structured into an arbitrary number of groups and interacts into an arbitrary number of patches where the infection takes place. In this framework, we model host mobility that depends on its epidemiological status, by a Lagrangian approach. This framework is applied to a general SEIRS model and the basic reproduction number $\mathcal{R_0}$ is derived. Read More


Background: Globally, influenza is a major cause of morbidity, hospitalization and mortality. Influenza vaccination has shown substantial protective effectiveness in the United States. We investigated state-level patterns of coverage rates of seasonal and pandemic influenza vaccination, among the overall population in the U. Read More


Background: Guillain-Barr\'e Syndrome (GBS) is a common type of severe acute paralytic neuropathy and associated with other virus infections such as dengue fever and Zika. This study investigate the relationship between GBS, dengue, local meteorological factors in Hong Kong and global climatic factors from January 2000 to June 2016. Methods: The correlations between GBS, dengue, Multivariate El Nino Southern Oscillation Index (MEI) and local meteorological data were explored by the Spearman Rank correlations and cross-correlations between these time series. Read More


The 1918 influenza pandemic was characterized by multiple epidemic waves. We investigated into reactive social distancing, a form of behavioral responses, and its effect on the multiple influenza waves in the United Kingdom. Two forms of reactive social distancing have been used in previous studies: Power function, which is a function of the proportion of recent influenza mortality in a population, and Hill function, which is a function of the actual number of recent influenza mortality. Read More


A selectivity theory is proposed to help explain how one gender of a species might tend to evolve with greater variability than the other gender. Briefly, the theory says that if one sex is relatively selective, then more variable subpopulations of the opposite sex will tend to prevail over those with lesser variability; and conversely, if one sex is relatively non-selective, then less variable subpopulations of the opposite sex will tend to prevail over those with greater variability. This theory makes no assumptions about differences in means between the sexes, nor does it presume that one sex is selective and the other non-selective. Read More


Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. Read More


What characteristics distinguish liars from truth-tellers? Recent research has explored "when" and "why" people lie. Yet little is known about "who" lies. Previous studies have led to mixed results about the effect of gender on deception, and they have largely neglected the role of other characteristics, such as age and level of education. Read More


We investigate the role of greed on the lifetime of a random-walking forager on an initially resource-rich lattice. Whenever the forager lands on a food-containing site, all the food there is eaten and the forager can hop $\mathcal{S}$ more steps without food before starving. Upon reaching an empty site, the forager comes one time unit closer to starvation. Read More


Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. Read More


In a recent paper published in Ecosphere, their authors suggest that extending the logistic growth model in its usual r - K parametrization to a multi-patch environment results in undesirable properties, that were referred to as the "perfect mixing paradox". This led the authors to recommend using the Verhulst r - {\alpha} parametrization of the logistic model instead and abandoning the term "carrying capacity" in the context of population dynamics. In this study we show that the use of the logistic equation in its traditional r - K parametrization is appropriate for representing the dynamics of populations in a simple spatial context with passive migration among patches. Read More


We first recall some basic facts from the theory of discrete-time Markov chains arising from two types neutral and non-neutral evolution models of population genetics with constant size. We then define and analyse a version of such models whose fluctuating total population size is conserved on average only. In our model, the population of interest is seen as being embedded in a frame process which is a critical Galton-Watson process. Read More


The propagation of a beneficial mutation in a spatially extended population is usually studied using the phenomenological stochastic Fisher-Kolmogorov (SFKPP) equation. We derive here an individual based, stochastic model founded on the spatial Moran process where fluctuations are treated exactly. At high selection pressure, the results of this model are different from the classical FKPP. Read More


Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily supplied by mutation (i.e. Read More


A key problem in modelling the evolution dynamics of infectious diseases is the mathematical representation of the mechanism of transmission of the contagion. Models with a finite number of subpopulations can be described via systems of ordinary differential equations. When dealing with populations with space structure the relevant quantities are spatial densities, whose evolution in time requires nonlinear partial differential equations, which are known as reaction-diffusion systems. Read More


The Zika virus has been found in individual cases but has not been confirmed as the cause of in the large number of cases of microcephaly in Brazil in 2015-6. Indeed, disparities between the incidence of Zika and microcephaly across geographic locations has led to questions about the virus's role. Here we consider whether the insecticide pyriproxyfen used in Brazilian drinking water might be the primary cause or a cofactor. Read More


We study the large population limit of a stochastic individual-based model which describes the time evolution of a diploid hermaphroditic population reproducing according to Mendelian rules. In [Neukirch, Bovier, 2016] it is proved that sexual reproduction allows unfit alleles to survive in individuals with mixed genotype much longer than they would in populations reproducing asexually. In the present paper we prove that this indeed opens the possibility that individuals with a pure genotype can reinvade in the population after the appearance of further mutations. Read More


In this note, we characterize the embeddability of general Kimura 3ST Markov matrices in terms of their eigenvalues. As a consequence, we are able to compute the volume of such matrices and compare it to the volume of all Markov matrices within the model. Moreover, we provide an example showing that, in general, mutation rates are not identifiable from substitution probabilities under the Kimura 3ST model. Read More


Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Read More


Understanding the influence of structure of dispersal network on the species persistence and modeling a much realistic species dispersal in nature are two central issues in spatial ecology. A realistic dispersal structure which favors the persistence of interacting ecological systems has been studied in [Holland \& Hastings, Nature, 456:792--795 (2008)], where it is shown that a randomization of the structure of dispersal network in a metapopulation model of prey and predator increases the species persistence via clustering, prolonged transient dynamics, and amplitudes of population fluctuations. In this paper, by contrast, we show that a deterministic network topology in a metapopulation can also favor asynchrony and prolonged transient dynamics if species dispersal obeys a long-range interaction governed by a distance-dependent power-law. Read More


The Ebola virus disease is a severe viral haemorrhagic fever syndrome caused by Ebola virus. This disease is transmitted by direct contact with the body fluids of an infected person and objects contaminated with virus or infected animals, with a death rate close to 90% in humans. Recently, some mathematical models have been presented to analyse the spread of the 2014 Ebola outbreak in West Africa. Read More


Understanding how desertification takes place in different ecosystems is an important step in attempting to forecast and prevent such transitions. Dryland ecosystems often exhibit patchy vegetation, which has been shown to be an important factor on the possible regime shifts that occur in arid regions in several model studies. In particular, both gradual shifts that occur by front propagation, and abrupt shifts where patches of vegetation vanish at once, are a possibility in dryland ecosystems due to their emergent spatial heterogeneity. Read More


In many natural situations one observes a local system with many competing species which is coupled by weak immigration to a regional species pool. The dynamics of such a system is dominated by its stable and uninvadable (SU) states. When the competition matrix is random, the number of SUs depends on the average value of its entries and the variance. Read More


High hydrostatic pressure is commonly encountered in many environments, but the effects of high pressure on eukaryotic cells have been understudied. To understand the effects of hydrostatic pressure in the model eukaryote, Saccharomyces cerevisiae, we have performed quantitative experiments of cell division, cell morphology, and cell death under a wide range of pressures. We developed an automated image analysis method for quantification of the yeast budding index - a measure of cell cycle state - as well as a continuum model of budding to investigate the effect of pressure on cell division and cell morphology. Read More


Despite its radical assumption of ecological equivalence between species, neutral biodiversity theory can often provide good fits to species abundance distributions observed in nature. Major criticisms of neutral theory have focused on interspecific differences, which are in conflict with ecological equivalence. However, individual-level neutrality in nature is also broken by differences between conspecific individuals at different life stages, which in many communities may vastly exceed interspecific differences between individuals at similar stages. Read More


Geographic structure can affect patterns of genetic differentiation and speciation rates. In this article, we investigate the dynamics of genetic distances in a geographically structured metapopulation. We model the metapopulation as a weighted directed graph, with N vertices corresponding to N homogeneous subpopulations. Read More