# Quantitative Biology - Populations and Evolution Publications (50)

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## Quantitative Biology - Populations and Evolution Publications

In recent health policy papers, the social sciences insist that given the increased risks of heart diseases, diabetes, and other chronic conditions women face worldwide, biomedical research should step away from reducing female health to female reproductive health. Arguably the global women's health agenda goes much beyond reproductive concerns, but we contend that it is mistaken to conceptualize women's health as separate from women's evolved reproductive system. This paper elaborates on the evolutionary question 'why do women menstruate?' to review the support for the hypothesis that cyclical immunity is central to the modulation of health and diseases in female bodies. Read More

A new statistical physics model is introduced for describing the interaction of bacteria with anti-microbial drugs (AMDs) which we show can reproduce qualitative features of the emergence of single and double anti-microbial resistance (AMR) through natural selection. The model portrays a lattice inhabited by agents, the latter modelled by simple Ising perceptrons. Model parameters and outputs are based on actual biological and pharmacological quantities, opening the possibility of comparing our results to controlled in vitro experiments. Read More

Containing the recent West African outbreak of Ebola virus (EBOV) required the deployment of substantial global resources. Operationally, health workers and surveillance teams treated cases, collected genetic samples, and tracked case contacts. Despite the substantial progress in analyzing and modeling EBOV epidemiological data, a complete characterization of the spatiotemporal spread of Ebola cases remains a challenge. Read More

The relationship between the M-species stochastic Lotka-Volterra competition (SLVC) model and the M-allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection and the Moran model with frequency-dependent selection (equivalently, a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model. Read More

This paper is devoted to the analysis of a simple Lotka-Volterra food chain evolving in a stochastic environment. It can be seen as the companion paper of Hening and Nguyen `17 where we have characterized the persistence and extinction of such a food chain under the assumption that there is no intraspecific competition among predators. In the current paper we focus on the case when all the species experience intracompetition. Read More

**Affiliations:**

^{1}Institute of Environmental Science and Technology, Universitat Autonoma de Barcelona,

^{2}Institute of Environmental Science and Technology, Universitat Autonoma de Barcelona

This paper proposes an approach to environmental accounting useful for studying the feasibility of socio-economic systems in relation to the external constraints posed by ecological compatibility. The approach is based on a multi-scale analysis of the metabolic pattern of ecosystems and societies and it provides an integrated characterization of the resulting interaction. The text starts with a theoretical part explaining (i) the implicit epistemological revolution implied by the notion of ecosystem metabolism and the fund-flow model developed by Georgescu-Roegen applied to environmental accounting, and (ii) the potentials of this approach to create indicators to assess ecological integrity and environmental impacts. Read More

We study Eigen's quasispecies model in the asymptotic regime where the length of the genotypes goes to infinity and the mutation probability goes to 0. A limiting infinite system of differential equations is obtained. We prove the convergence of the trajectories, as well as the convergence of the equilibrium solutions. Read More

In recent years there has been a growing interest in the study of the dynamics of stochastic populations. A key question in population biology is to understand the conditions under which populations coexist or go extinct. Theoretical and empirical studies have shown that coexistence can be facilitated or negated by both biotic interactions and environmental fluctuations. Read More

Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted gene tree topologies is ASTRAL. In this paper, we derive theoretical sample complexity results for the number of genes required by ASTRAL to guarantee reconstruction of the correct species tree with high probability. Read More

Genome-wide association studies (GWAS) in humans are revealing the genetic architecture of biomedical, life history and anthropomorphic traits, i.e., the frequencies and effect sizes of variants contributing to heritable variation in a trait. Read More

This paper analyses the dynamics of infectious disease with a concurrent spread of disease awareness. The model includes local awareness due to contacts with aware individuals, as well as global awareness due to reported cases of infection and awareness campaigns. We investigate the effects of time delay in response of unaware individuals to available information on the epidemic dynamics by establishing conditions for the Hopf bifurcation of the endemic steady state of the model. Read More

We investigate the dynamics of a greedy forager that moves by random walking in an environment where each site initially contains one unit of food. Upon encountering a food-containing site, the forager eats all the food there and can subsequently hop an additional $\mathcal{S}$ steps without food before starving to death. Upon encountering an empty site, the forager goes hungry and comes one time unit closer to starvation. Read More

We investigate global stability properties of a HIV/AIDS population model with constant recruitment rate, mass action incidence, and variable population size. Existence and uniqueness results for disease-free and endemic equilibrium points are proved. Global stability of the equilibria is obtained through Lyapunov's direct method and LaSalle's invariance principle. Read More

Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. Number of identified sequences in the reference databases affects the precision of identification. Read More

Most infectious diseases including more than half of known human pathogens are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a single epidemic propagating in multiple species and compare and contrast it with the endemic steady state of the disease. We use the two-species Susceptible-Infected-Recovered (SIR) model to calculate the severity of post-epidemic collapses in populations of two host species as a function of their initial population sizes, the times individuals remain infectious, and the matrix of infection rates. Read More

The use of computers in statistical physics is common because the sheer number of equations that describe the behavior of an entire system particle by particle often makes it impossible to solve them exactly. Monte Carlo methods form a particularly important class of numerical methods for solving problems in statistical physics. Although these methods are simple in principle, their proper use requires a good command of statistical mechanics, as well as considerable computational resources. Read More

Even this saying itself is a variant of a similar statement attributed to Bernard of Chartres in the 12th Century, and inspired the title for a book by Steven Hawking and an album by Oasis. Creative ideas beget other creative ideas and, as a result, modifications accumulate, and we see an overall increase in the complexity of cultural novelty over time, a phenomenon sometimes referred to as the ratchet effect (Tomasello, Kruger, & Ratner, 1993). Although we may never meet the people or objects that creatively influence us, by assimilating what we encounter around us and bringing to bear our own insights and perspectives, we all contribute in our own way, however small, to a second evolutionary process -- the evolution of culture. Read More

Energy saving mechanisms in nature allow following organisms to expend less energy than leaders. Queues, or ordered rows of individuals, may form when organisms exploit the available energy saving mechanism while travelling at near-maximal sustainable metabolic capacities; compact clusters form when group members travel well below maximal sustainable metabolic capacities. The group size range, given here as the ratio of the difference between the size of the largest and smallest group members, and the size of the largest member (as a per cent), has been hypothesized to correspond proportionately to the energy saving quantity because weaker, smaller, individuals sustain speeds of stronger, larger, individuals by exploiting the energy saving mechanism (as a per cent). Read More

Synergies between evolutionary game theory and statistical physics have significantly improved our understanding of public cooperation in structured populations. Multiplex networks, in particular, provide the theoretical framework within network science that allows us to mathematically describe the rich structure of interactions characterizing human societies. While research has shown that multiplex networks may enhance the resilience of cooperation, the interplay between the overlap in the structure of the layers and the control parameters of the corresponding games has not yet been investigated. Read More

We investigate the rates of drug resistance acquisition in a natural population using molecular epidemiological data from Bolivia. First, we study the rate of direct acquisition of double resistance from the double sensitive state within patients and compare it to the rates of evolution to single resistance. In particular, we address whether or not double resistance can evolve directly from a double sensitive state within a given host. Read More

Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the probabilities of splits on gene trees under the multispecies coalescent model, and how their features might inform species tree inference. After investigating the behavior of split consensus methods, we investigate split invariants --- that is, polynomial relationships between split probabilities. Read More

We use optimal control theory with the purpose of finding the best spraying policy with the aim of at least to minimize and possibly to eradicate the number of parasites, i.e., the prey for the spiders living in an agroecosystems. Read More

Gene drives have the potential to rapidly replace a harmful wild-type allele with a gene drive allele engineered to have desired functionalities. However, an accidental or premature release of a gene drive construct to the natural environment could damage an ecosystem irreversibly. Thus, it is important to understand the spatiotemporal consequences of the super-Mendelian population genetics prior to potential applications. Read More

In a standard bifurcation of a dynamical system, the stationary points (or more generally attractors) change qualitatively when varying a control parameter. Here we describe a novel unusual effect, when the change of a parameter, e.g. Read More

Following \cite{ipel1}, we consider a nonlinear SIS-type nonlocal system describing the spread of epidemics on networks, assuming nonlimited transmission, We prove local existence of a unique solution for any diffusion coefficients and global existence in the case of equal diffusion coefficients. Next we study the asymptotic behaviour of the solution and show that the disease-free equilibrium (DFE) is linearly and globally asymptotically stable when the total mean population is small. Finally, we prove that the solution of the system converge to the $DFE$. Read More

Desertification in dryland ecosystems is considered to be a major environmental threat that may lead to devastating consequences. The concern increases when the system admits two alternative steady states and the transition is abrupt and irreversible (catastrophic shift). However, recent studies show that the inherent stochasticity of the birth-death process, when superimposed on the presence of an absorbing state, may lead to a continuous (second order) transition even if the deterministic dynamics supports a catastrophic transition. Read More

We investigate the impact of misinformation about the contact structure on the ability to predict disease outbreaks. We base our study on 31 empirical temporal networks and tune the frequencies in errors in the node identities or timestamps of contacts. We find that for both these spreading scenarios, the maximal misprediction of both the outbreak size and time to extinction follows an stretched exponential convergence as a function of the error frequency. Read More

We consider excursions for a class of stochastic processes describing a population of discrete individuals experiencing density-limited growth, such that the population has a finite carrying capacity and behaves qualitatively like the classical logistic model when the carrying capacity is large. Being discrete and stochastic, however, our population nonetheless goes extinct in finite time. We present results concerning the maximum of the population prior to extinction in the large population limit, from which we obtain establishment probabilities and upper bounds for the process, as well as estimates for the waiting time to establishment and extinction. Read More

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An {\em unrooted} phylogenetic network on a finite set $X$ of taxa, or {\em network}, is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is $X$. It is called a {\em phylogenetic tree} if the underlying graph is a tree. Read More

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of inferring large trees from rooted triple and quartet data. These methods can be applied in new statistically consistent procedures for inference of a species tree from gene trees under the multispecies coalescent model. Read More

Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering a linear response to it, a common proportionality in such expression changes was derived and partially verified by experimental data. Here, we examined global protein expression in {\it Escherichia coli} under various environmental perturbations. Read More

Epidemic spreading has been intensively studied in SIS epidemic model. Although the mean-field theory of SIS model has been widely used in the research, there is a lack of comparative results between different theoretical calculations, and the differences between them should be systematically explained. In this paper, we have compared different theoretical solutions for mean-field theory and explained the underlying reason. Read More

We prove a result which makes explicit the requirement that a multiplicatively-closed Markov model must form a Lie algebra Read More

UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that minimizes the minimum evolution score relative to the dissimilarity matrix among all rooted trees with the same leaf-set in which all leaves have the same distance to the root. We prove that the NEME problem is NP-hard. Read More

The process of desertification in the semi-arid climatic zone is considered by many as a catastrophic regime shift, since the positive feedback of vegetation density on growth rates yields a system that supports alternative steady states. Here we present a large-scale analysis of vegetation \emph{dynamics} for $~2.5 \ 10^6 \ \rm{km}^2$ of the African Sahel region, with spatial resolution of $30 \times 30$ meters, using three consecutive snapshots. Read More

Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. A typical example is the evolution of mating systems in plant species. In this work, we present a probabilistic modeling framework for binary trait, random species trees, in which the number of species and their traits are represented by a two-type, continuous time Markov branching process. Read More

In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Read More

In this report we document our findings from deploying 88 cameras on 13 islands from 2014-2016. We collected 92,694 photographs across 18,721 trap nights, including 3,591 wildlife events and 1,070 carnivore events. We had a mean of 6. Read More

Background: Over the past few decades, numerous forecasting methods have been proposed in the field of epidemic forecasting. Such methods can be classified into different categories such as deterministic vs. probabilistic, comparative methods vs. Read More

Biological populations are subject to fluctuating environmental conditions. Different adaptive strategies can allow them to cope with these fluctuations: specialization to one particular environmental condition, adoption of a generalist phenotype that compromise between conditions, or population-wise diversification (bet-hedging). Which strategy provides the largest selective advantage in the long run depends on the range of accessible phenotypes and the statistics of the environmental fluctuations. Read More

An SEIRS epidemic with disease fatalities is introduced in a growing population (modelled as a super-critical linear birth and death process). The study of the initial phase of the epidemic is stochastic, while the analysis of the major outbreaks is deterministic. Depending on the values of the parameters, the following scenarios are possible. Read More

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent "wave" of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Read More

The present paper deals with a prey-predator model with prey refuge proportion to both species and independent harvesting of each species. Our study shows that using refuge as control, it can break the limit circle of the system and reach the required state of equilibrium level. It is established the optimal harvesting policy. Read More

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