Vaguery + population-biology   45

Polygenic scores and tea drinking | gcbias
Some of these complications are perhaps best illustrated with a toy example. Say we perform a GWAS of the amount of tea that individuals in the UK drink (e.g. in the UK Biobank). On the basis of this tea GWAS, someone (let’s call him Bob) could claim that we could learn about France-UK differences in tea consumption by just counting up the average number of alleles for tea preference that individuals in the UK and France carry. If the British, overall, are more likely to have alleles that increase tea consumption than French people, then Bob might say that we have demonstrated that the difference between French and UK people’s preference for tea is in part genetic. Bob would assure us that these alleles are polymorphic in both countries, and that both environment and culture plays a role. He would further reassure us that there’ll be an overlapping distribution of tea drinking preferences in both countries, so he’s not saying that all British people drink more tea for genetic reasons. He’ll tell us he’s simply interested in showing that the average difference in tea consumption is partly genetic.
genetics  bioinformatics  GWAS  good-example  nature-and-nurture-sittin-in-a-tree  population-biology  cultural-norms 
7 weeks ago by Vaguery
[1808.05875] Co-evolution of nodes and links: diversity driven coexistence in cyclic competition of three species
When three species compete cyclically in a well-mixed, stochastic system of N individuals, extinction is known to typically occur at times scaling as the system size N. This happens, for example, in rock-paper-scissors games or conserved Lotka-Volterra models in which every pair of individuals can interact on a complete graph. Here we show that if the competing individuals also have a "social temperament" to be either introverted or extroverted, leading them to cut or add links respectively, then long-living state in which all species coexist can occur when both introverts and extroverts are present. These states are non-equilibrium quasi-steady states, maintained by a subtle balance between species competition and network dynamcis. Remarkably, much of the phenomena is embodied in a mean-field description. However, an intuitive understanding of why diversity stabilizes the co-evolving node and link dynamics remains an open issue.
coevolution  theoretical-biology  rather-interesting  population-biology  social-norms  to-write-about  to-simulate  artificial-life  it's-more-complicated-than-you-think  complexology  agent-based 
august 2018 by Vaguery
Estimating barriers to gene flow from distorted isolation by distance patterns | bioRxiv
In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.
population-biology  theoretical-biology  rather-interesting  simulation  to-write-about  consider:feature-discovery 
march 2018 by Vaguery
[1404.6520] How to partition diversity
Diversity measurement underpins the study of biological systems, but measures used vary across disciplines. Despite their common use and broad utility, no unified framework has emerged for measuring, comparing and partitioning diversity. The introduction of information theory into diversity measurement has laid the foundations, but the framework is incomplete without the ability to partition diversity, which is central to fundamental questions across the life sciences: How do we prioritise communities for conservation? How do we identify reservoirs and sources of pathogenic organisms? How do we measure ecological disturbance arising from climate change?
The lack of a common framework means that diversity measures from different fields have conflicting fundamental properties, allowing conclusions reached to depend on the measure chosen. This conflict is unnecessary and unhelpful. A mathematically consistent framework would transform disparate fields by delivering scientific insights in a common language. It would also allow the transfer of theoretical and practical developments between fields.
We meet this need, providing a versatile unified framework for partitioning biological diversity. It encompasses any kind of similarity between individuals, from functional to genetic, allowing comparisons between qualitatively different kinds of diversity. Where existing partitioning measures aggregate information across the whole population, our approach permits the direct comparison of subcommunities, allowing us to pinpoint distinct, diverse or representative subcommunities and investigate population substructure. The framework is provided as a ready-to-use R package to easily test our approach.
diversity  population-biology  bioinformatics  philosophy-of-science  algorithms  statistics  rather-interesting  to-write-about  to-understand  consider:genetic-programming  define-your-terms 
february 2018 by Vaguery
Variability in fitness effects and the limitations of lineage selection | bioRxiv
Natural selection is sensitive not only to the effect of a trait on total number of offspring produced but also to how a trait affects an individual's entire lineage of descendants. Here we show how a large number of seemingly disparate evolutionary problems, including sex, evolvability, and cooperation, all share the property that fitness varies among members of a lineage. This feature makes it difficult to summarize the evolutionary fate of an allele based solely on its effects on individual reproduction. We show that attempts to average over this variability are often justified, but can sometimes cause misleading results. We then describe a number of intriguing new evolutionary phenomena that have emerged in studies that explicitly model the fate of alleles that influence long-term lineage dynamics. We conclude with prospects for generalizations of population genetics theory and discuss how this theory might be applied to the evolution of infectious diseases.
population-biology  evolutionary-biology  agent-based  fitness  define-your-terms  rather-interesting  to-write-about  consider:effects-in-GAs 
february 2017 by Vaguery
Genotypic complexity of Fisher's geometric model | bioRxiv
Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Here we compute the probability that a pair of randomly chosen mutations interacts sign-epistatically, which is found to decrease algebraically with increasing phenotypic dimension n, and varies non-monotonically with the distance from the phenotypic optimum. We then derive asymptotic expressions for the mean number of fitness maxima in genotypic landscapes composed of all combinations of L random mutations. This number increases exponentially with L, and the corresponding growth rate is used as a measure of the complexity of the genotypic landscape. The dependence of the complexity on the parameters of the model is found to be surprisingly rich, and three distinct phases characterized by different landscape structures are identified. The complexity generally decreases with increasing phenotypic dimension, but a non-monotonic dependence on n is found in certain regimes. Our results inform the interpretation of experiments where the parameters of Fisher's model have been inferred from data, and help to elucidate which features of empirical fitness landscapes can (or cannot) be described by this model.
population-biology  theoretical-biology  theory-and-practice-sitting-in-a-tree  fitness-landscapes  models-and-modes  to-write-about  nudge-targets  consider:rediscovery  consider:robustness  consider:multiobjective-versions 
january 2017 by Vaguery
[1605.08717] Predicting patterns of long-term adaptation and extinction with population genetics
Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But extinction can result from failure to adapt not only to catastrophes, but also to a backlog of environmental challenges. We model long-term evolution to long series of small challenges, where fitter populations reach higher population sizes. The population's long-term fitness dynamic is well approximated by a simple stochastic Markov chain model. Long-term persistence occurs when the rate of adaptation exceeds the rate of environmental deterioration for some genotypes. Long-term persistence times are consistent with typical fossil species persistence times of several million years. Immediately preceding extinction, fitness declines rapidly, appearing as though a catastrophe disrupted a stably established population, even though gradual evolutionary processes are responsible. New populations go through an establishment phase where, despite being demographically viable, their extinction risk is elevated. Should the population survive long enough, extinction risk later becomes constant over time.
theoretical-biology  population-biology  self-organization  complex-systems  power-laws  nudge-targets  consider:stress-testing  consider:simulation 
june 2016 by Vaguery
[1504.03832] Almost all random graphs are amplifiers of selection for Birth-death dynamics, but suppressors of selection for death-Birth dynamics
We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of selection are graphs for which the fixation probability is increased for advantageous mutants and decreased for disadvantageous mutants. A few examples of such amplifiers have been developed, but so far it is unclear how many such structures exist and how to construct them. Here, we show that almost any random graph is an amplifier of selection for Birth-death updating, where an individual is selected to reproduce with probability proportional to its fitness and one of its neighbors is replaced by that offspring at random. If we instead focus on death-Birth updating, in which a random individual is removed and its neighbors compete for the empty spot, then the same ensemble of graphs consists of almost only suppressors of selection for which the fixation probability is decreased for advantageous mutants and increased for disadvantageous mutants. This shows that in order to explore the impact of population structure on evolutionary dynamics, it is crucial to take the details of the microscopic evolutionary process into account.
theoretical-biology  population-biology  graph-theory  simulation  nonlinear-dynamics  biases  rather-interesting 
march 2016 by Vaguery
[1508.01453] Asymptotic Green's function for the stochastic reproduction of competing variants via Fisher's angular transformation
The Wright-Fisher Fokker-Planck equation describes the stochastic dynamics of self-reproducing, competing variants at fixed population size. We use Fisher's angular transformation, which defines a natural length for this stochastic process, to remove the co-ordinate dependence of it's diffusive dynamics, resulting in simple Brownian motion in an unstable potential, driving variants to extinction or fixation. This insight allows calculation of very accurate asymptotic formula for the Green's function under neutrality and selection, using a novel heuristic Gaussian approximation.
population-biology  theoretical-biology  fitness-landscapes  nudge-targets  consider:looking-to-see 
february 2016 by Vaguery
[1507.08245] Epistasis and the structure of fitness landscapes: are experimental fitness landscapes compatible with Fisher's model?
The fitness landscape defines the relationship between genotypes and fitness in a given environment, and underlies fundamental quantities such as the distribution of selection coefficient, or the magnitude and type of epistasis. A better understanding of variation of landscape structure across species and environments is thus necessary to understand and predict how populations adapt. An increasing number of experiments access the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is biased by the protocol used to identify mutations. Here we develop a rigorous and flexible statistical framework based on Approximate Bayesian Computation to address these concerns, and use this framework to fit a broad class of phenotypic fitness models (including Fisher's model) to 24 empirical landscapes representing 9 diverse biological systems. In spite of uncertainty due to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness of fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible model in only 3 out of 9 biological systems. In most cases, including notably the landscapes of drug resistance, Fisher's model is not able to explain the structure of empirical landscapes and patterns of epistasis.
fitness-landscapes  looking-to-see  theory-and-practice-sitting-in-a-tree  theoretical-biology  population-biology  modeling-is-not-mathematics 
february 2016 by Vaguery
[1509.01194] A mathematical analysis of the evolutionary benefits of sexual reproduction
The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key must lie in the creation of increased variability in offspring, causing enhanced response to selection. Rigorously quantifying the effects of assorted mechanisms which might lead to such increased variability, and establishing that these beneficial effects outweigh the immediate costs of sexual reproduction has, however, proved problematic. Here we introduce an approach which does not focus on particular mechanisms influencing factors such as the fixation of beneficial mutants or the ability of populations to deal with deleterious mutations, but rather tracks the entire distribution of a population of genotypes as it moves across vast fitness landscapes. In this setting simulations now show sex robustly outperforming asex across a broad spectrum of finite or infinite population models. Concentrating on the additive infinite populations model, we are able to give a rigorous mathematical proof establishing that sexual reproduction acts as a more efficient optimiser of mean fitness, thereby solving the problem for this model. Some of the key features of this analysis carry through to the finite populations case.
population-biology  theoretical-biology  simple-models-of-the-evolution  fitness-landscapes  open-questions-that-aren't-especially-open 
february 2016 by Vaguery
[1602.03093] The effect of environmental stochasticity on species richness in neutral communities
Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic and comprehensive discussion of these two contradicting tendencies, using the metacommunity version of the recently proposed time-average neutral model of biodiversity which incorporates environmental stochasticity and demographic noise and allows for extinction and speciation. We show that the incorporation of demographic noise into the model is essential to its applicability, yielding realistic behavior of the system when fitness variations are relatively weak. The dependence of species richness on the strength of environmental stochasticity changes sign when the correlation time of the environmental variations increases. This transition marks the point at which the storage effect no longer succeeds in stabilizing the community.
fitness-landscapes  community-formation  diversity  theoretical-biology  population-biology  rather-interesting  to-write-about 
february 2016 by Vaguery
[1506.06572] Stochastic evolutionary games in dynamic populations
Frequency dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model, which naturally combines these two evolutionary ingredients by assuming frequency dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population and thus the population size is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by the deterministic competitive Lotka-Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. As the population size is driven by the fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size, the population would thrive regardless of its average payoff.
population-biology  game-theory  signal-processing  stochastic-resonance  simulation  rather-interesting  generalization  nudge-targets  consider:looking-to-see 
february 2016 by Vaguery
[1411.6322] The Complexity of Genetic Diversity
A key question in biological systems is whether genetic diversity persists in the long run under evolutionary competition or whether a single dominant genotype emerges. Classic work by Kalmus in 1945 has established that even in simple diploid species (species with two chromosomes) diversity can be guaranteed as long as the heterozygote individuals enjoy a selective advantage. Despite the classic nature of the problem, as we move towards increasingly polymorphic traits (e.g. human blood types) predicting diversity and understanding its implications is still not fully understood. Our key contribution is to establish complexity theoretic hardness results implying that even in the textbook case of single locus diploid models predicting whether diversity survives or not given its fitness landscape is algorithmically intractable. We complement our results by establishing that under randomly chosen fitness landscapes diversity survives with significant probability. Our results are structurally robust along several dimensions (e.g., choice of parameter distribution, different definitions of stability/persistence, restriction to typical subclasses of fitness landscapes). Technically, our results exploit connections between game theory, nonlinear dynamical systems, complexity theory and biology and establish hardness results for predicting the evolution of a deterministic variant of the well known multiplicative weights update algorithm in symmetric coordination games which could be of independent interest.
population-biology  fitness-landscapes  starting-to-actually-get-mad-about-them  to-fix 
february 2016 by Vaguery
[1505.06108] General formulation of Luria-Delbr{"u}ck distribution of the number of mutants
The Luria-Delbr{\"u}ck experiment is a cornerstone of evolutionary theory, demonstrating the randomness of mutations before selection. The distribution of the number of mutants in this experiment has been the subject of intense investigation during the last 70 years. Despite this considerable effort, most of the results have been obtained under the assumption of constant growth rate, which is far from the experimental condition. We derive here the properties of this distribution for arbitrary growth function, for both the deterministic and stochastic growth of the mutants. The derivation we propose uses the number of wild type bacteria as the independent variable instead of time. The derivation is surprisingly simple and versatile, allowing many generalizations to be taken easily into account.
population-biology  mutation  theoretical-biology  modeling-is-not-mathematics  experiment  consider:impact-on-folk-fitness 
december 2015 by Vaguery
Convergent Evolution During Local Adaptation to Patchy Landscapes | bioRxiv
Species often encounter, and adapt to, many patches of locally similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise and spread in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the degree of constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies a model of the balance between these two routes to adaptation in continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel, locally adapted allele to appear in a patch of habitat where it is favored through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? How can we tell which has occurred, i.e., what population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration--selection equilibrium surrounding an already adapted patch, in particular treating those rare families that reach new patches as spatial branching processes. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example.
evolutionary-biology  population-biology  adaptation  biology  rather-interesting  experiment  models 
september 2015 by Vaguery
[1501.04497] Food web assembly rules
In food webs, many interacting species coexist despite the restrictions imposed by the competitive exclusion principle and apparent competition. For the generalized Lotka-Volterra equations, sustainable coexistence necessitates nonzero determinant of the interaction matrix. Here we show that this requirement is equivalent to demanding that each species be part of a non-overlapping pairing, which substantially constrains the food web structure. We demonstrate that a stable food web can always be obtained if a non-overlapping pairing exists. If it does not, the matrix rank can be used to quantify the lack of niches, corresponding to unpaired species. For the species richness at each trophic level, we derive the food web assembly rules, which specify sustainable combinations. In neighboring levels, these rules allow the higher level to avert competitive exclusion at the lower, thereby incorporating apparent competition. In agreement with data, the assembly rules predict high species numbers at intermediate levels and thinning at the top and bottom. Using comprehensive food web data, we demonstrate how omnivores or parasites with hosts at multiple trophic levels can loosen the constraints and help obtain coexistence in food webs. Hence, omnivory may be the glue that keeps communities intact even under extinction or ecological release of species.
hey-I-know-this-guy  food-webs  community-assembly  theoretical-biology  population-biology  ecology  simulation  self-organization  nudge-targets  rather-interesting 
july 2015 by Vaguery
Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues. | bioRxiv
Development is a process that needs to tightly coordinated in both space and time. Cell tracking and lineage tracing have become important experimental techniques in developmental biology and allow us to map the fate of cells and their progeny in both space and time. A generic feature of developing (as well as homeostatic) tissues that these analyses have revealed is that relatively few cells give rise to the bulk of the cells in a tissue; the lineages of most cells come to an end fairly quickly. This has spurned the interest also of computational and theoretical biologists/physicists who have developed a range of modelling -- perhaps most notably are the agent-based modelling (ABM) --- approaches. These can become computationally prohibitively expensive but seem to capture some of the features observed in experiments. Here we develop a complementary perspective that allows us to understand the dynamics leading to the formation of a tissue (or colony of cells). Borrowing from the rich population genetics literature we develop genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We apply this approach to tissues that grow under confined conditions --- as would, for example, be appropriate for the neural crest --- and unbounded growth --- illustrative of the behaviour of 2D tumours or bacterial colonies. The classical coalescent model from population genetics is readily adapted to capture tissue genealogies for different models of tissue growth and development. We show that simple but universal scaling relationships allow us to establish relationships between the coalescent and different fractal growth models that have been extensively studied in many different contexts, including developmental biology. Using our genealogical perspective we are able to study the statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations.
theoretical-biology  developmental-biology  evo-devo  artificial-life  population-biology  self-organization  rather-interesting  morphology  fitness-landscapes  nudge-targets  consider:detailed-reexamination 
july 2015 by Vaguery
[1403.6333] Range Expansion of Heterogeneous Populations
Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.
population-biology  microbiology  rather-interesting  simulation  artificial-life  nudge-targets  consider:rediscovery  consider:feature-discovery  consider:looking-to-see 
july 2015 by Vaguery
[1312.6321] The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection
Virophages are viruses that rely on the replication machinery of other viruses to reproduce within eukaryotic hosts. Two different modes of coinfection have been posited based on experimental observation. In one mode, the virophage and virus enter the host independently. In the other mode, the virophage adheres to the virus so both virophage and virus enter the host together. Here we ask: what are the ecological effects of these different modes of coinfection? In particular, what ecological effects are common to both infection modes, and what are the differences particular to each mode? We develop a pair of biophysically motivated ODE models of viral-host population dynamics, corresponding to dynamics arising from each mode of infection. We find both modes of coinfection allow for the coexistence of the virophage, virus, and host either at a stable fixed point or through cyclical dynamics. In both models, virophage tend to be the most abundant population and their presence always reduces the viral abundance and increases the host abundance. However, we do find qualitative differences between models. For example, via extensive sampling of biologically relevant parameter space, we only observe bistability when the virophage and virus enter the host together. We discuss how such differences may be leveraged to help identify modes of infection in natural environments from population level data.
population-biology  medical-technology  nonlinear-dynamics  competition  theoretical-biology  nudge-targets  systems-biology  biological-engineering 
november 2014 by Vaguery
When is selection effective? | bioRxiv
Deleterious alleles are more likely to reach high frequency in small populations because of chance fluctuations in allele frequency. This may lead, over time, to reduced average fitness in the population. In that sense, selection is more `effective' in larger populations. Many recent studies have considered whether the different demographic histories across human populations have resulted in differences in the number, distribution, and severity of deleterious variants, leading to an animated debate. This article seeks to clarify some terms of the debate by identifying differences in definitions and assumptions used in these studies and providing an intuitive explanation for the observed similarity in genetic load among populations. The intuition is verified through analytical and numerical calculations. First, even though rare variants contribute to load, they contribute little to load differences across populations. Second, the accumulation of non-recessive load after a bottleneck is slow for the weakly deleterious variants that contribute much of the long-term variation among populations. Whereas a bottleneck increases drift instantly, it affects selection only indirectly, so that fitness differences can keep accumulating long after a bottleneck is over. Third, drift and selection tend to have opposite effects on load differentiation under dominance models. Because of this competition, load differences across populations depend sensitively and intricately on past demographic events and on the distribution of fitness effects. A given bottleneck can lead to increased or decreased load for variants with identical fitness effects, depending on the subsequent population history. Because of this sensitivity, both classical population genetic intuition and detailed simulations are required to understand differences in load across populations.
theoretical-biology  population-biology  philosophy-of-science  rather-interesting  define-your-terms  what-selection-"is"-for-example 
november 2014 by Vaguery
Social evolution and genetic interactions in the short and long term | bioRxiv
The evolution of social traits remains one of the most fascinating and feisty topics in evolutionary biology even after half a century of theoretical research. W. D. Hamilton shaped much of the field initially with his 1964 papers that laid out the foundation for understanding the effect of genetic relatedness on the evolution of social behavior. Early theoretical investigations revealed two critical assumptions required for Hamilton's rule to hold in dynamical models: weak selection and additive genetic interactions. However, only recently have analytical approaches from population genetics and evolutionary game theory developed sufficiently so that social evolution can be studied under the joint action of selection, mutation, and genetic drift. We review how these approaches suggest two timescales for evolution under weak mutation: (i) a short-term timescale where evolution occurs between a finite set of alleles, and (ii) a long-term timescale where a continuum of alleles are possible and populations evolve continuously from one monomorphic trait to another. We show how Hamilton's rule emerges from the short-term analysis under additivity and how non-additive genetic interactions can be accounted for more generally. This short-term approach reproduces, synthesizes, and generalizes many previous results including the one-third law from evolutionary game theory and risk dominance from economic game theory. Using the long-term approach, we illustrate how trait evolution can be described with a diffusion equation that is a stochastic analogue of the canonical equation of adaptive dynamics. Peaks in the stationary distribution of the diffusion capture classic notions of convergence stability from evolutionary game theory and generally depend on the additive genetic interactions inherent in Hamilton's rule. Surprisingly, the peaks of the long-term stationary distribution can predict the effects of simple kinds of non-additive interactions. Additionally, the peaks may capture the effect of both weak and strong selection in a manner analogous to classic diffusion approaches in population genetics. Together, the results from the short and long-term approaches suggest both how Hamilton's insight may be robust in unexpected ways and how current analytical approaches can expand our understanding of social evolution far beyond Hamilton's original work.
theoretical-biology  population-biology  social-dynamics  feisty  nudge-targets  consider:open-ended-exploration 
november 2014 by Vaguery
[1408.5007] A Consistent Estimator of the Evolutionary Rate
We consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate L, conditioned on the observed number of particles to be equal n. Particles are assumed to move independently on the real line according to the Brownian motion with the local variance s2. In this paper we treat n particles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimator Rn2 of the evolutionary rate r2=s2/L. The estimator Rn2 is proportional to the sample variance Sn2 computed from n trait values. We find an approximate formula for the standard error of Rn2 based on a neat asymptotic relation for the variance of Sn2.
population-biology  evolutionary-biology  statistics  estimation  inference  interesting  consider:use-in-evolutionary-algorithms 
october 2014 by Vaguery
[1401.4040] A Wright-Fisher model with indirect selection
We define and study two mathematical models of a surprising biological strategy where some individuals adopt a behaviour that is harmful to others without any direct advantage for themselves. The first model covers a single reproductive season, and is mathematically a mix between samplings with and without replacement; its analysis is done by a sort of "reverse numerical analysis", viewing a key recurrence relation as a discretization scheme for a PDE. This model is then used as a building block for a variant of the classical Wright-Fisher model. In the large population limit, we prove the convergence of the renormalized process to a diffusion with a frequency dependent drift. This allows a quantitative comparison of the indirect selective advantage with the direct one classically considered in the Wright-Fisher model.
population-biology  counterintuitive  the-mangle-in-practice  evolution  nudge-targets  consider:stress-testing  consider:rediscovery  consider:walking-there 
august 2014 by Vaguery
[1402.6354] A tug-of-war between driver and passenger mutations in cancer and other adaptive processes
Cancer progression is an example of a rapid adaptive process where evolving new traits is essential for survival and requires a high mutation rate. Precancerous cells acquire a few key mutations that drive rapid population growth and carcinogenesis. Cancer genomics demonstrates that these few 'driver' mutations occur alongside thousands of random 'passenger' mutations-a natural consequence of cancer's elevated mutation rate. Some passengers can be deleterious to cancer cells, yet have been largely ignored in cancer research. In population genetics, however, the accumulation of mildly deleterious mutations has been shown to cause population meltdown. Here we develop a stochastic population model where beneficial drivers engage in a tug-of-war with frequent mildly deleterious passengers. These passengers present a barrier to cancer progression that is described by a critical population size, below which most lesions fail to progress, and a critical mutation rate, above which cancers meltdown. We find support for the model in cancer age-incidence and cancer genomics data that also allow us to estimate the fitness advantage of drivers and fitness costs of passengers. We identify two regimes of adaptive evolutionary dynamics and use these regimes to rationalize successes and failures of different treatment strategies. We find that a tumor's load of deleterious passengers can explain previously paradoxical treatment outcomes and suggest that it could potentially serve as a biomarker of response to mutagenic therapies. Collective deleterious effect of passengers is currently an unexploited therapeutic target. We discuss how their effects might be exacerbated by both current and future therapies.
theoretical-biology  population-biology  cancer  simulation  diversity  nudge-targets  Wright-it-ain't 
july 2014 by Vaguery
[1309.0657] Human Genome Variation and the concept of Genotype Networks
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of systems such as metabolic networks and RNA folds. Recently, they have been the base for re-conciliating the two neutralist and selectionist schools on evolution.
Here, we adapted the concept of genotype networks to the study of population genetics data, applying them to the 1000 Genomes dataset. We used networks composed of short haplotypes of Single Nucleotide Variants (SNV), and defined phenotypes as the presence or absence of a haplotype in a human population. We used coalescent simulations to determine if the number of samples in the 1000 Genomes dataset is large enough to represent the genetic variation of real populations. The result is a scan of how properties related to the genetic heterogeneity and stability to mutations are distributed along the human genome. We found that genes involved in acquired immunity, such as some HLA and MHC genes, tend to have the most heterogeneous and connected networks; and we have also found that there is a small, but significant difference between networks of coding regions and those of non-coding regions, suggesting that coding regions are both richer in genotype diversity, and more stable to mutations. Together, the work presented here may constitute a starting point for applying genotype networks to study genome variation, as larger datasets of next-generation data will become availa
bioinformatics  diversity  networks  population-biology  GWAS  interesting 
february 2014 by Vaguery
[1311.2435] The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we studied the invasion of beneficial mutations responsible for Escherichia coli's adaptation to the mouse gut and demonstrate the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where a similar adaptive mutation arises repeatedly on different haplotypes without reaching fixation. The genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly in most populations, we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate.
genetics  microbiology  microflora  microbial-ecology  experiment  population-biology  interesting 
december 2013 by Vaguery
[1309.1152] The inevitability of unconditionally deleterious substitutions during adaptation
Studies on the genetics of adaptation typically neglect the possibility that a deleterious mutation might fix. Nonetheless, here we show that, in many regimes, the first substitution is most often deleterious, even when fitness is expected to increase in the long term. In particular, we prove that this phenomenon occurs under weak mutation for any house-of-cards model with an equilibrium distribution. We find that the same qualitative results hold under Fisher's geometric model. We also provide a simple intuition for the surprising prevalence of unconditionally deleterious substitutions during early adaptation. Importantly, the phenomenon we describe occurs on fitness landscapes without any local maxima and is therefore distinct from "valley-crossing". Our results imply that the common practice of ignoring deleterious substitutions leads to qualitatively incorrect predictions in many regimes. Our results also have implications for the substitution process at equilibrium and for the response to a sudden decrease in population size.
fitness-landscapes  theoretical-biology  population-biology  alma-maters  nudge-targets 
november 2013 by Vaguery
[1310.8091] Role of detritus in a spatial food web model with diffusion
One of the central themes in modern ecology is the enduring debate on whether there is a relationship between the complexity of a biological community and its stability. In this paper, we focus on the role of detritus and spatial dispersion on the stability of ecosystems. Using Monte Carlo simulations we analyze two three level models of food webs: a grazing one with the basal species (i.e. primary producers) having unlimited food resources and a detrital one in which the basal species uses detritus as a food resource. While the vast majority of theoretical studies neglects detritus, from our results it follows that the detrital food web is more stable than its grazing counterpart, because the interactions mediated by detritus dump out fluctuations in species' densities. Since the detritus model is the more complex one in terms of interaction patterns, our results provide new evidence for the advocates of the complexity as one of the factors enhancing stability of ecosystems.
theoretical-biology  population-biology  ecology  simulation  models  nudge-targets 
november 2013 by Vaguery
[1309.3772] A Gene Regulatory Model of heterosis and speciation
Crossing individuals from genetically distinct populations often results in improvements in quantitative traits, such as growth rate, biomass production and stress resistance; this phenomenon is known as heterosis. We have taken a computational approach to explore the mechanisms underlying heterosis, developing a simulation of evolution and hybridization of Gene Regulatory Networks (GRNs) in a Boolean framework. These artificial regulatory networks exhibit biologically realistic topological properties and fitness is measured as the ability of a network to respond to external inputs in the correct way. Our model reproduced experimental observations from the literature on heterosis using only biologically meaningful parameters, such as mutation rates. Hybrid vigor was observed, its extent was seen to increase as parental populations diverged until it collapses when the two populations have become incompatible. Thus, the model also describes a process of speciation and links it to collapsing hybrid fitness due to genetic incompatibility of the separated populations. We also reproduce for the first time in a model the fact that hybrid vigor cannot easily be fixed by crossing hybrids, which is currently an important drawback of the use of hybrid crops. The simulation allows us to study the effects of three standard models for the genetic basis of heterosis, dominance, over-dominance, and epistasis. In our simulation over-dominance is the main factor contributing to hybrid vigour, whereas under-dominance and epistatic incompatibility are responsible for the fitness collapse. As the parental populations diverge, a single mutation can determine an almost sudden incompatibility leading to low fitness hybrids.
epistasis  Kauffmania  boolean-networks  theoretical-biology  population-biology  actually-quite-interesting  nudge-targets  artificial-life  hybrid-vigor 
september 2013 by Vaguery
[1309.3312] Universality and predictability in the evolution of molecular quantitative traits
Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. Here we discuss recent developments in the evolutionary theory of quantitative traits that reach beyond classical quantitative genetics. We focus on universal evolutionary characteristics: these are largely independent of a trait's genetic basis, which is often at least partially unknown. We show that universal measurements can be used to infer selection on a quantitative trait, which determines its evolutionary mode of conservation or adaptation. Furthermore, universality is closely linked to predictability of trait evolution across lineages. We argue that universal trait statistics extends over a range of cellular scales and opens new avenues of quantitative evolutionary systems biology.
fitness-landscapes  evolutionary-biology  population-biology  quantitative-biology  complexology  neutral-networks  meh? 
september 2013 by Vaguery
[1306.1652] On the accumulation of deleterious mutations during range expansions
We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations co-segregate. We perform individual-based simulations of a uniform linear habitat and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load thousands of generations after the expansion. Our results extend qualitatively and quantitatively to two-dimensional expansions. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyze patterns of neutral and non-neutral genetic diversity in humans and find an excellent fit between theory and data.
population-biology  evolution  simulation  experiment 
july 2013 by Vaguery
[1307.4789] Reproductive Value in Graph-structured Populations
Evolutionary graph theory has grown to be an area of intense study. Despite the amount of interest in the field, it seems to have grown separate from other subfields of population genetics and evolution. In the current work I introduce the concept of Fisher's (1930) reproductive value into the study of evolution on graphs. Reproductive value is a measure of the expected genetic contribution of an individual to a distant future generation. In a heterogeneous graph-structured population, differences in the number of connections among individuals translates into differences in the expected number of offspring, even if all individuals have the same fecundity. These differences are accounted for by reproductive value. The introduction of reproductive value permits the calculation of the fixation probability of a mutant in a neutral evolutionary process in any graph-structured population for either the moran birth-death or death-birth process.
population-biology  social-networks  agent-based  context  you-need-not-just-the-motive-but-the-means-my-boy 
july 2013 by Vaguery
[1301.0004] Population genetics of gene function
This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of an organism, this observation contributes to extend the population-genetical characterisation of biological function. To support this statement a mathematical relation is derived to link the lifetime ratio T_1/T_2, which parametrizes the different survival ability of two phenotypes, with population variables that quantify the amount of neutral variation underlying a population's phenotypic distribution.
population-biology  theoretical-biology  evolution  life-histories  nudge-targets  fitness-landscapes  contingency  define-your-terms-project 
april 2013 by Vaguery
[1302.4267] Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems
Biological systems show two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity: the near decomposability of the system into modules with distinct functionality. Recent work suggests that modularity can evolve in a variety of circumstances, including goals that vary in time such that they share the same subgoals (modularly varying goals). Here, we studied the origin of modularity and sparseness focusing on the nature of the mutation process, rather than variations in the goal. We use simulations of evolution with different mutation rules. We find that commonly used sum-rule mutations, in which interactions are mutated by adding random numbers, do not lead to modularity or sparseness except for special situations. In contrast, product-rule mutations in which interactions are mutated by multiplying by random numbers, a better model for the effects of biological mutations, lead to sparseness naturally. When the goals of evolution are modular, in the sense that specific groups of inputs affect specific groups of outputs, product-rule mutations lead to modular structure; sum-rule mutations do not. Product-rule mutations generate sparseness and modularity because they keep small interaction terms small.
theoretical-biology  population-biology  systems-biology  robustness  nudge-targets  resilience  network-theory  interesting 
april 2013 by Vaguery
Guest post: Natural selection in real time via road kill « Why Evolution Is True
A new paper in Current Biology by Charles & Mary Brown with the folksy title, “Where has all the road kill gone?“  reports evidence for rapid evolution of wing length in cliff swallows (Petrochelidon pyrrhonota) nesting on highway overpasses in Nebraska. (See also this news piece on Science‘s website.) For those evolution-deniers who demand to see natural selection in “real time,” this is one bit of evidence.
evolution  population-biology  examples  selection-in-action 
march 2013 by Vaguery
[1211.3609] Neutral selection
Hubbell's neutral theory of biodiversity has successfully explained the observed composition of many ecological communities but it relies on strict demographic equivalence among species and provides no room for evolutionary processes like selection, adaptation and speciation. Here we show how to embed the neutral theory within the Darwinian framework. In a fitness landscape with a quadratic maximum, typical of quantitative traits, selection restricts the extant species to have traits close to optimal, so that the fitness differences between surviving species are small. For sufficiently small mutation steps, the community structure fits perfectly to the Fisher log-series species abundance distribution. The theory is relatively insensitive to moderate amounts of environmental noise, wherein the location of the fitness maximum changes by amounts of order the width of the noise-free distribution. Adding very large environmental noise to the model qualitatively changes the abundance distributions, converting the exponential fall-off of large species to a power-law decay, typical of a neutral model with environmental noise.
fitness-landscapes  population-biology  theoretical-biology  nudge-targets  simulation 
march 2013 by Vaguery
[1208.3185] Genealogies of rapidly adapting populations
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or infrequent evolutionary force. However, many species, particularly pathogens, are under continuous pressure to adapt in response to changing environments. A statistical framework for inference from diversity data of such populations is currently lacking. Toward this goal, we explore the properties of genealogies in a model of continual adaptation in asexual populations. We show that lineages trace back to a small pool of highly fit ancestors, in which almost simultaneous coalescence of more than two lineages frequently occurs. While such multiple mergers are unlikely under the neutral coalescent, they create a unique genetic footprint in adapting populations. The site frequency spectrum of derived neutral alleles, for example, is non-monotonic and has a peak at high frequencies, whereas Tajima's D becomes more and more negative with increasing sample size. Since multiple merger coalescents emerge in many models of rapid adaptation, we argue that they should be considered as a null-model for adapting populations.
population-biology  experiment  agent-based  simulation  nudge-targets  consider-as-a-feature-extraction-problem 
march 2013 by Vaguery
[1208.4973] Growth, competition and cooperation in spatial population genetics
We study an individual based model describing competition in space between two different alleles. Although the model is similar in spirit to classic models of spatial population genetics such as the stepping stone model, here however space is continuous and the total density of competing individuals fluctuates due to demographic stochasticity. By means of analytics and numerical simulations, we study the behavior of fixation probabilities, fixation times, and heterozygosity, in a neutral setting and in cases where the two species can compete or cooperate. By concluding with examples in which individuals are transported by fluid flows, we argue that this model is a natural choice to describe competition in marine environments.
population-biology  genetics  agent-based  simulation  complexology 
march 2013 by Vaguery
[1203.3884] A complex speciation-richness relationship in a simple neutral model
Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities and focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. Also, we use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is found to be the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.
evo-eco  community-formation  speciation  diversity  population-biology  models  nudge-targets 
august 2012 by Vaguery
[1208.0518] The efficacy of group selection is increased by coexistence dynamics within groups
Selection on the level of loosely associated groups has been suggested as a route towards the evolution of cooperation between individuals and the subsequent formation of higher-level biological entities. Such group selection explanations remain problematic, however, due to the narrow range of parameters under which they can overturn within-group selection that favours selfish behaviour. In principle, individual selection could act on such parameters so as to strengthen the force of between-group selection and hence increase cooperation and individual fitness, as illustrated in our previous work. However, such a process cannot operate in parameter regions where group selection effects are totally absent, since there would be no selective gradient to follow. One key parameter, which when increased often rapidly causes group selection effects to tend to zero, is initial group size, for when groups are formed randomly then even moderately sized groups lack significant variance in their composition. However, the consequent restriction of any group selection effect to small sized groups is derived from models that assume selfish types will competitively exclude their more cooperative counterparts at within-group equilibrium. In such cases, diversity in the migrant pool can tend to zero and accordingly variance in group composition cannot be generated. In contrast, we show that if within-group dynamics lead to a stable coexistence of selfish and cooperative types, then the range of group sizes showing some effect of group selection is much larger.
evolution  population-biology  theoretical-biology  group-selection  special-cases 
august 2012 by Vaguery
[1205.0665] What ecological factors shape species-area curves in neutral models?
Understanding factors that shape biodiversity and species coexistence across scales is of utmost importance in ecology, both theoretically and for conservation policies. Species-area relationships (SARs), measuring how the number of observed species increases upon enlarging the sampled area, constitute a convenient tool for quantifying the spatial structure of biodiversity. While general features of species-area curves are quite universal across ecosystems, some quantitative aspects can change significantly. Several attempts have been made to link these variations to ecological forces. Within the framework of spatially explicit neutral models, here we scrutinize the effect of varying the local population size (i.e. the number of individuals per site) and the level of habitat saturation (allowing for empty sites). We conclude that species-area curves become shallower when the local population size increases, while habitat saturation, unless strongly violated, plays a marginal role. Our findings provide a plausible explanation of why SARs for microorganisms are flatter than those for larger organisms.
biodiversity  population-biology  simulation  neutral-evolution  evolutionary-biology 
august 2012 by Vaguery
[1208.0482] The concurrent evolution of cooperation and the population structures that support it
"The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior."
agent-based  evolutionary-algorithms  evolutionary-economics  game-theory  population-biology 
august 2012 by Vaguery
[1205.2059] Emergence of clones in sexual populations
"In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection, populations consist of a diverse mixture of many genotypes, as is observed in many populations. In the opposite regime, which is realized for example in the facultatively sexual populations that outcross in only a fraction of reproductive cycles, selection can amplify individual genotypes into large clones. Such clones emerge when the fitness advantage of some of the genotypes is large enough that they grow to a significant fraction of the population despite being broken down by recombination. The occurrence of this "clonal condensation" depends, in addition to the outcrossing rate, on the heritability of fitness. Clonal condensation leads to a strong genetic heterogeneity of the population which is not adequately described by traditional population genetics measures, such as Linkage Disequilibrium. Here we point out the similarity between clonal condensation and the freezing transition in the Random Energy Model of spin glasses. Guided by this analogy we explicitly calculate the probability, Y, that two individuals are genetically identical as a function of the key parameters of the model. While Y is the analog of the spin-glass order parameter, it is also closely related to rate of coalescence in population genetics: Two individuals that are part of the same clone have a recent common ancestor."
population-biology  evolutionary-dynamics  finite-size-effects  models-and-modes 
august 2012 by Vaguery
[1203.3367] Stochastic differential equations for evolutionary dynamics with demographic noise and mutations
"We present a general framework to describe the evolutionary dynamics of an arbitrary number of types in finite populations based on stochastic differential equations (SDE). For large, but finite populations this allows to include demographic noise without requiring explicit simulations. Instead, the population size only rescales the amplitude of the noise. Moreover, this framework admits the inclusion of mutations between different types, provided that mutation rates, $mu$, are not too small compared to the inverse population size 1/N. This ensures that all types are almost always represented in the population and that the occasional extinction of one type does not result in an extended absence of that type. For $mu Nll1$ this limits the use of SDE's, but in this case there are well established alternative approximations based on time scale separation. We illustrate our approach by a Rock-Scissors-Paper game with mutations, where we demonstrate excellent agreement with simulation based results for sufficiently large populations. In the absence of mutations the excellent agreement extends to small population sizes."
finite-size-effects  population-biology  noise-in-design  nudge-targets 
july 2012 by Vaguery

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