scholarly journals Selection and Drift in Subdivided Populations: A Straightforward Method for Deriving Diffusion Approximations and Applications Involving Dominance, Selfing and Local Extinctions

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2153-2166 ◽  
Author(s):  
Denis Roze ◽  
François Rousset
Keyword(s):  
Fitness Function ◽  
Structured Populations ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Diffusion Approximations ◽  
Simple Method ◽  
Straightforward Method ◽  
Subdivided Populations ◽  
Local Extinctions ◽  
Fixation Probabilities

AbstractPopulation structure affects the relative influence of selection and drift on the change in allele frequencies. Several models have been proposed recently, using diffusion approximations to calculate fixation probabilities, fixation times, and equilibrium properties of subdivided populations. We propose here a simple method to construct diffusion approximations in structured populations; it relies on general expressions for the expectation and variance in allele frequency change over one generation, in terms of partial derivatives of a “fitness function” and probabilities of genetic identity evaluated in a neutral model. In the limit of a very large number of demes, these probabilities can be expressed as functions of average allele frequencies in the metapopulation, provided that coalescence occurs on two different timescales, which is the case in the island model. We then use the method to derive expressions for the probability of fixation of new mutations, as a function of their dominance coefficient, the rate of partial selfing, and the rate of deme extinction. We obtain more precise approximations than those derived by recent work, in particular (but not only) when deme sizes are small. Comparisons with simulations show that the method gives good results as long as migration is stronger than selection.

scholarly journals A simple method to estimate the in-house limit of detection for genetic mutations with low allele frequencies in whole-exome sequencing analysis by next-generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takumi Miura ◽  
Satoshi Yasuda ◽  
Yoji Sato
Keyword(s):  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Somatic Mutations ◽  
Limit Of Detection ◽  
Allele Frequencies ◽  
Genetic Mutations ◽  
Sequencing Data ◽  
Simple Method ◽  
Whole Exome ◽  
Generation Sequencing

Abstract Background Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency. Results Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%. Conclusions For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.

scholarly journals Selection, Subdivision and Extinction and Recolonization

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 1105-1114 ◽  
Author(s):  
Joshua L Cherry
Keyword(s):  
Frequency Dependence ◽  
Allele Frequency ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Theoretical Predictions ◽  
Subdivided Populations ◽  
Fixation Probabilities ◽  
Selection Parameters ◽  
To Come ◽  
Do So

Abstract In a subdivided population, the interaction between natural selection and stochastic change in allele frequency is affected by the occurrence of local extinction and subsequent recolonization. The relative importance of selection can be diminished by this additional source of stochastic change in allele frequency. Results are presented for subdivided populations with extinction and recolonization where there is more than one founding allele after extinction, where these may tend to come from the same source deme, where the number of founding alleles is variable or the founders make unequal contributions, and where there is dominance for fitness or local frequency dependence. The behavior of a selected allele in a subdivided population is in all these situations approximately the same as that of an allele with different selection parameters in an unstructured population with a different size. The magnitude of the quantity Nese, which determines fixation probability in the case of genic selection, is always decreased by extinction and recolonization, so that deleterious alleles are more likely to fix and advantageous alleles less likely to do so. The importance of dominance or frequency dependence is also altered by extinction and recolonization. Computer simulations confirm that the theoretical predictions of both fixation probabilities and mean times to fixation are good approximations.

scholarly journals Bpop: an efficient program for estimating base population allele frequencies in single and multiple group structured populations

2020 ◽  
Vol 29 (3) ◽  
Author(s):  
Ismo Stranden ◽  
Esa A. Mäntysaari
Keyword(s):  
Computing Time ◽  
Large Data ◽  
Generalized Least Squares ◽  
Structured Populations ◽  
Allele Frequencies ◽  
Data Sets ◽  
Dense Matrix ◽  
Base Population ◽  
Multiple Group ◽  
Efficient Program

Base population allele frequencies (AF) should be used in genomic evaluations. A program named Bpop was implemented to estimate base population AF using a generalized least squares (GLS) method when the base population individuals can be assigned to groups. The required dense matrix products involving (A22 )-1v were implemented efficiently using sparse submatrices of A-1, where A and A22 are pedigree relationship matrices for all and genotyped animals, respectively. Three approaches were implemented: iteration on pedigree (IOP), iteration in memory (IM), and direct inversion by sparsity preserving Cholesky decomposition (CHM). The test data had 1.5 million animals genotyped using 50240 markers. Total computing time (the product (A22)-11) was 53 min (1.2 min) by IOP, 51 min (0.3 min) by IM, and 56 min (4.6 min) by CHM. Peak computer core memory use was 0.67 GB by IOP, 0.80 GB by IM, and 7.53 GB by CHM. Thus, the IOP and IM approaches can be recommended for large data sets because of their low memory use and computing time.

scholarly journals Evolution of cooperation in an epithelium

2019 ◽  
Vol 16 (152) ◽  
pp. 20180918 ◽  
Author(s):  
Jessie Renton ◽  
Karen M. Page
Keyword(s):  
Social Interactions ◽  
Voronoi Tessellation ◽  
Evolutionary Game ◽  
Cellular Level ◽  
Structured Populations ◽  
Evolution Of Cooperation ◽  
Animal Kingdom ◽  
Population Structures ◽  
Fixation Probabilities ◽  
Evolutionary Graph Theory

Cooperation is prevalent in nature, not only in the context of social interactions within the animal kingdom but also on the cellular level. In cancer, for example, tumour cells can cooperate by producing growth factors. The evolution of cooperation has traditionally been studied for well-mixed populations under the framework of evolutionary game theory, and more recently for structured populations using evolutionary graph theory (EGT). The population structures arising due to cellular arrangement in tissues, however, are dynamic and thus cannot be accurately represented by either of these frameworks. In this work, we compare the conditions for cooperative success in an epithelium modelled using EGT, to those in a mechanical model of an epithelium—the Voronoi tessellation (VT) model. Crucially, in this latter model, cells are able to move, and birth and death are not spatially coupled. We calculate fixation probabilities in the VT model through simulation and an approximate analytic technique and show that this leads to stronger promotion of cooperation in comparison with the EGT model.

When a Fly Has to Fly to Reproduce: Selection against Conditional Recessive Lethals in Drosophila

2010 ◽  
Vol 72 (1) ◽  
pp. 12-15 ◽  
Author(s):  
Andrea D. Plunkett ◽  
Lev Y. Yampolsky
Keyword(s):  
Drosophila Melanogaster ◽  
Allele Frequency ◽  
Experimental Model ◽  
Food Source ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Evolutionary Patterns ◽  
Visible Marker ◽  
Meaningful Comparison ◽  
Marker Alleles

We propose an experimental model suitable for demonstrating allele frequency change in Drosophila melanogaster populations caused by selection against an easily scorable conditional lethal, namely recessive flightless alleles such as apterous and vestigial. Homozygotes for these alleles are excluded from reproduction because the food source used to establish each generation is accessible only by flight. The observed dynamics of flightless-allele frequencies generally follows the theoretically predicted pattern, with slight deviation toward less intense selection. We also suggest observing selection against flight-independent visible marker alleles in the same population as a meaningful comparison. The proposed experiments can easily be scheduled within one semester, and the expected data provide ample opportunities for discussion of quantitative evolutionary patterns.

A Simple Method for Measuring Muffler Transmission Loss With PU Probes

2013 ◽  
Author(s):  
Li Yan ◽  
Weikang Jiang
Keyword(s):  
Transfer Matrix ◽  
Particle Velocity ◽  
Transmission Loss ◽  
Low Frequency ◽  
Frequency Measurement ◽  
Decomposition Methods ◽  
Simple Method ◽  
Straightforward Method ◽  
Alternative Approach ◽  
Set Up

The conventional approaches for measuring muffler transmission loss based on measurement in impedance tube are mainly decomposition methods and transfer matrix method. The decomposition method needs an anechoic termination, but it is not easy in some cases particularly for low frequency measurement. Two-load method and two-source method based on transfer matrix techniques are considered to be an alternative approach which does not require an anechoic termination. PU probe can measure both sound pressure and particle velocity, which is applied to some acoustic measurement such as absorption coefficient in recent years. A straightforward method for measuring muffler transmission loss by two PU probes measuring particle velocity at the inlet and outlet of muffler is presented. The four-pole parameters of the muffler can be calculated directly. The transmission loss measured by the PU method agrees well with the result measured by conventional four-pole method and FEM result. To instruct the approach, the influence of measurement distance between PU probe and the inlet or outlet of muffler and ambient noise are analyzed, which gives comprehensive suggestions for measurement set up.

LOCAL EXTINCTIONS, CONNECTEDNESS, AND CULTURAL EVOLUTION IN STRUCTURED POPULATIONS

2012 ◽  
Vol 15 (01n02) ◽  
pp. 1150002 ◽  
Author(s):  
L. S. PREMO
Keyword(s):  
Cultural Transmission ◽  
Structured Populations ◽  
Local Extinction ◽  
Upper Paleolithic ◽  
Spatially Explicit ◽  
Neutral Genetic Diversity ◽  
The Social ◽  
Local Extinctions ◽  
Number Of Individuals ◽  
Total Diversity

Population geneticists have shown that the effects of local extinction and recolonization on selectively neutral genetic diversity are sensitive to the number of individuals that migrate between groups. Here, we employ a spatially explicit metapopulation model to investigate the extent to which the effects of local extinction on selectively neutral cultural diversity and change are sensitive to intergroup cultural transmission — the rate at which cultural variants are transmitted between groups. Our results show that the level of intergroup cultural transmission as well as the topology of the social network that mediates cultural transmission between groups influence the way in which local extinctions affect total diversity, group differentiation, and the rate at which copy errors accumulate in structured populations. The results are discussed in the context of the archaeological record of Middle and Upper Paleolithic societies.

scholarly journals Modelling optimal behavioural strategies in structured populations using a novel theoretical framework

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andrew Morozov ◽  
Oleg A. Kuzenkov ◽  
Elena G. Arashkevich
Keyword(s):  
Developmental Stages ◽  
Fitness Function ◽  
Natural Populations ◽  
Theoretical Framework ◽  
Structured Populations ◽  
Theoretical Modelling ◽  
Structured Population Model ◽  
Definition Of ◽  
Evolutionary Fitness ◽  
Behavioural Strategies

Abstract Understanding complex behavioural patterns of organisms observed in nature can be facilitated using mathematical modelling. The conventional paradigm in animal behavior modelling consists of maximisation of some evolutionary fitness function. However, the definition of fitness of an organism or population is generally subjective, and using different criteria can lead us to contradictory model predictions regarding optimal behaviour. Moreover, structuring of natural populations in terms of individual size or developmental stage creates an extra challenge for theoretical modelling. Here we revisit and formalise the definition of evolutionary fitness to describe long-term selection of strategies in deterministic self-replicating systems for generic modelling settings which involve an arbitrary function space of inherited strategies. Then we show how optimal behavioural strategies can be obtained for different developmental stages in a generic von-Foerster stage-structured population model with an arbitrary mortality term. We implement our theoretical framework to explore patterns of optimal diel vertical migration (DVM) of two dominant zooplankton species in the north-eastern Black Sea. We parameterise the model using 7 years of empirical data from 2007-2014 and show that the observed DVM can be explained as the result of a trade-off between depth-dependent metabolic costs for grazers, anoxia zones, available food, and visual predation.

scholarly journals Allele frequency dynamics in a pedigreed natural population

2018 ◽  
Vol 116 (6) ◽  
pp. 2158-2164 ◽  
Author(s):  
Nancy Chen ◽  
Ivan Juric ◽  
Elissa J. Cosgrove ◽  
Reed Bowman ◽  
John W. Fitzpatrick ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Success ◽  
Allele Frequency ◽  
Natural Population ◽  
Allele Frequencies ◽  
Frequency Change ◽  
Short Term ◽  
Individual Survival ◽  
Frequency Changes ◽  
Genetic Contributions

A central goal of population genetics is to understand how genetic drift, natural selection, and gene flow shape allele frequencies through time. However, the actual processes underlying these changes—variation in individual survival, reproductive success, and movement—are often difficult to quantify. Fully understanding these processes requires the population pedigree, the set of relationships among all individuals in the population through time. Here, we use extensive pedigree and genomic information from a long-studied natural population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of different evolutionary processes in shaping patterns of genetic variation through time. We performed gene dropping simulations to estimate individual genetic contributions to the population and model drift on the known pedigree. We found that observed allele frequency changes are generally well predicted by accounting for the different genetic contributions of founders. Our results show that the genetic contribution of recent immigrants is substantial, with some large allele frequency shifts that otherwise may have been attributed to selection actually due to gene flow. We identified a few SNPs under directional short-term selection after appropriately accounting for gene flow. Using models that account for changes in population size, we partitioned the proportion of variance in allele frequency change through time. Observed allele frequency changes are primarily due to variation in survival and reproductive success, with gene flow making a smaller contribution. This study provides one of the most complete descriptions of short-term evolutionary change in allele frequencies in a natural population to date.

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