scholarly journals Toward a universal model for spatially structured populations

2020 ◽  
Author(s):  
Loïc Marrec ◽  
Irene Lamberti ◽  
Anne-Florence Bitbol
Keyword(s):  
Population Structure ◽  
Natural Selection ◽  
Migration Rate ◽  
Structured Populations ◽  
Microbial Populations ◽  
Star Graph ◽  
Apparent Paradox ◽  
Constant Size ◽  
Rate Asymmetry ◽  
Large Populations

Microbial populations often have complex spatial structures, with homogeneous competition holding only at a local scale. Population structure can strongly impact evolution, in particular by affecting the fixation probability of mutants. Here, we propose a model of structured microbial populations on graphs, where each node of the graph contains a well-mixed deme whose size can fluctuate, and where migrations are independent from birth and death events. We study analytically and numerically the mutant fixation probabilities in different structures, in the rare migration regime. In particular, we demonstrate that the star graph continuously transitions between amplifying and suppressing natural selection as migration rate asymmetry is varied. This elucidates the apparent paradox in existing constant-size models on graphs, where the star is an amplifier or a suppressor depending on the details of the dynamics or update rule chosen, e.g. whether each birth event precedes or follows a death event. The celebrated amplification property of the star graph for large populations is preserved in our model, for specific migration asymmetry. We further demonstrate a general mapping between our model and constant-size models on graphs, under a constraint on migration rates, which directly stems from assuming constant size. By lifting this constraint, our model reconciles and generalizes previous results, showing that migration rate asymmetry is key to determining whether a given population structure amplifies or suppresses natural selection.

Outbreeding depression is uncommon and predictable

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Natural Selection ◽  
Genetic Differences ◽  
Outbreeding Depression ◽  
Isolated Populations ◽  
Large Populations

Crosses between populations within species sometimes result in reduced fitness, especially in F2 and later generations (outbreeding depression). The primary mechanisms causing outbreeding depression in crosses between populations are fixed chromosomal differences and adaptive genetic differences, especially for long-isolated populations. Outbreeding depression is usually observed after crossing populations with ploidy differences or fixed differences for translocations, inversions or centric fusions: the magnitudes are usually ploidy > translocations and monobrachial centric fusions > inversions and simple centric fusions. Populations adapted to different environments (but with the same karyotype) often exhibit outbreeding depression when crossed, especially in the F2 and later generations. Even if outbreeding depression occurs, it is often only temporary, as natural selection acts to remove it, especially in large populations.

scholarly journals Population structure, gene flow and natural selection in populations of Euphydryas phaeton

Heredity ◽  
1975 ◽  
Vol 34 (3) ◽  
pp. 407-415 ◽  
Author(s):  
Peter F Brussard ◽  
A Thomas Vawter
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Natural Selection

scholarly journals Physical interactions reduce the power of natural selection in growing yeast colonies

2018 ◽  
Vol 115 (45) ◽  
pp. 11448-11453 ◽  
Author(s):  
Andrea Giometto ◽  
David R. Nelson ◽  
Andrew W. Murray
Keyword(s):  
Natural Selection ◽  
Continuum Model ◽  
Microbial Populations ◽  
Mechanical Forces ◽  
Time Varying ◽  
Drug Resistant ◽  
Yeast Strains ◽  
Physical Interactions ◽  
Varying Environments ◽  
Doubling Times

Microbial populations often assemble in dense populations in which proliferating individuals exert mechanical forces on the nearby cells. Here, we use yeast strains whose doubling times depend differently on temperature to show that physical interactions among cells affect the competition between different genotypes in growing yeast colonies. Our experiments demonstrate that these physical interactions have two related effects: they cause the prolonged survival of slower-growing strains at the actively-growing frontier of the colony and cause faster-growing strains to increase their frequency more slowly than expected in the absence of physical interactions. These effects also promote the survival of slower-growing strains and the maintenance of genetic diversity in colonies grown in time-varying environments. A continuum model inspired by overdamped hydrodynamics reproduces the experiments and predicts that the strength of natural selection depends on the width of the actively growing layer at the colony frontier. We verify these predictions experimentally. The reduced power of natural selection observed here may favor the maintenance of drug-resistant cells in microbial populations and could explain the apparent neutrality of interclone competition within tumors.

scholarly journals A novel coalescent method insensitive to population structure

2020 ◽  
Author(s):  
Zeqi Yao ◽  
Kehui Liu ◽  
Shanjun Deng ◽  
Xionglei He
Keyword(s):  
Population Structure ◽  
Phylogenetic Tree ◽  
Simulated Data ◽  
Structured Populations ◽  
Population History ◽  
Cell Populations ◽  
Developmental History ◽  
Coalescent Analysis ◽  
History Of ◽  
Larger Sample

AbstractConventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation (one generation back) is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. i-coalescent analysis computes the instantaneous coalescent rate (iCR) by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

scholarly journals Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

scholarly journals Ordering structured populations in multiplayer cooperation games

2015 ◽  
Author(s):  
Jorge Peña ◽  
Bin Wu ◽  
Arne Traulsen
Keyword(s):  
Population Structure ◽  
Spatial Structure ◽  
Structured Populations ◽  
Evolution Of Cooperation ◽  
Multiplayer Games ◽  
Spatial Games ◽  
Population Structures ◽  
Single Structure ◽  
Containment Order ◽  
Update Rules

AbstractSpatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure 𝒮1 is greater than population structure 𝒮2 in the containment or the volume order, then 𝒮1 can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated.

scholarly journals The Price equation and reproductive value

2020 ◽  
Vol 375 (1797) ◽  
pp. 20190356 ◽  
Author(s):  
Alan Grafen
Keyword(s):  
Natural Selection ◽  
Fundamental Theorem ◽  
Structured Populations ◽  
Reproductive Value ◽  
Price Equation ◽  
Class Structure ◽  
Theme Issue ◽  
Starting Point ◽  
Important Idea ◽  
Fisher’S Fundamental Theorem

The Price equation is widely recognized as capturing conceptually important properties of natural selection, and is often used to derive versions of Fisher’s fundamental theorem of natural selection, the secondary theorems of natural selection and other significant results. However, class structure is not usually incorporated into these arguments. From the starting point of Fisher’s original connection between fitness and reproductive value, a principled way of incorporating reproductive value and structured populations into the Price equation is explained, with its implications for precise meanings of (two distinct kinds of) reproductive value and of fitness. Once the Price equation applies to structured populations, then the other equations follow. The fundamental theorem itself has a special place among these equations, not only because it always incorporated class structure (and its method is followed for general class structures), but also because that is the result that justifies the important idea that these equations identify the effect of natural selection. The precise definitions of reproductive value and fitness have striking and unexpected features. However, a theoretical challenge emerges from the articulation of Fisher’s structure: is it possible to retain the ecological properties of fitness as well as its evolutionary out-of-equilibrium properties? This article is part of the theme issue ‘Fifty years of the Price equation’.

scholarly journals Stochastic Epidemic Models in Structured Populations Featuring Dynamic Vaccination and Isolation

2007 ◽  
Vol 44 (03) ◽  
pp. 571-585 ◽  
Author(s):  
Frank Ball ◽  
Philip D. O'Neill ◽  
James Pike
Keyword(s):  
Exposure Period ◽  
Structured Populations ◽  
Infectious Period ◽  
Stochastic Comparison ◽  
Threshold Parameter ◽  
Final Size ◽  
Period Distribution ◽  
Comparison Results ◽  
Stochastic Epidemic ◽  
Large Populations

We consider a stochastic model for the spread of an SEIR (susceptible → exposed → infective → removed) epidemic among a population of individuals partitioned into households. The model incorporates both vaccination and isolation in response to the detection of cases. When the infectious period is exponential, we derive an explicit formula for a threshold parameter, and analytic results that enable computation of the probability of the epidemic taking off. These quantities are found to be independent of the exposure period distribution. An approximation for the expected final size of an epidemic that takes off is obtained, evaluated numerically, and found to be reasonably accurate in large populations. When the infectious period is not exponential, but has an increasing hazard rate, we obtain stochastic comparison results in the case where the exposure period is fixed. Our main result shows that as the exposure period increases, both the severity of the epidemic in a single household and the threshold parameter decrease, under certain assumptions concerning isolation. Corresponding results for infectious periods with decreasing hazard rates are also derived.

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