scholarly journals Spread of new mutations through space

2022 ◽  
Author(s):  
Kyle Shaw ◽  
Peter Beerli
Keyword(s):  
Population Density ◽  
Population Size ◽  
Simulation Software ◽  
Effective Population ◽  
Random Drift ◽  
Rate Of Spread ◽  
Large Populations ◽  
Discrete Population ◽  
Explicit Simulation ◽  
New Mutations

The terms population size and population density are often used interchangeably, when in fact they are quite different. When viewed in a spatial landscape, density is defined as the number of individuals within a square unit of distance, while population size is simply the total count of a population. In discrete population genetics models, the effective population size is known to influence the interaction between selection and random drift with selection playing a larger role in large populations while random drift has more influence in smaller populations. Using a spatially explicit simulation software we investigate how population density affects the flow of new mutations through a geographical space. Using population density, selectional advantage, and dispersal distributions, a model is developed to predict the speed at which the new allele will travel, obtaining more accurate results than current diffusion approximations provide. We note that the rate at which a neutral mutation spreads begins to decay over time while the rate of spread of an advantageous allele remains constant. We also show that new advantageous mutations spread faster in dense populations.

Adjustment of fecundity and sex ratio in response to social environments in a haplodiploid mite

2022 ◽  
Author(s):  
Nuwan Weerawansha ◽  
Qiao Wang ◽  
Xiong Zhao He
Keyword(s):  
Population Density ◽  
Sex Ratio ◽  
Population Size ◽  
Local Population ◽  
Female Offspring ◽  
Social Environments ◽  
Positive Interaction ◽  
Offspring Sex Ratio ◽  
Offspring Sex ◽  
Large Populations

Animals can adjust reproductive strategies in favour of corporation or competition in response to local population size and density, the two key factors of social environments. However, previous studies usually focus on either population size or density but ignore their interactions. Using a haplodiploid spider mite, Tetranychus ludeni Zacher, we carried out a factorial experiment in the laboratory to examine how ovipositing females adjust their fecundity and offspring sex ratio during their early reproductive life under various population size and density. We reveal that females laid significantly more eggs with increasing population size and significantly fewer eggs with increasing population density. This suggests that large populations favour cooperation between individuals and dense populations increase competition. We demonstrate a significant negative interaction of population size and density that resulted in significantly fewer eggs laid in the large and dense populations. Furthermore, we show that females significantly skewed the offspring sex ratio towards female-biased in small populations to reduce the local mate competition among their sons. However, population density incurred no significant impact on offspring sex ratio, while the significant positive interaction of population size and density significantly increased the proportion of female offspring in the large and dense populations, which will minimise food or space competition as females usually disperse after mating at crowded conditions. These results also suggest that population density affecting sex allocation in T. ludeni is intercorrelated with population size. This study provides evidence that animals can manipulate their reproductive output and adjust offspring sex ratio in response to various social environments, and the interactions of different socio-environmental factors may play significant roles.

scholarly journals The population genetics of haplo-diploids and X-linked genes

1984 ◽  
Vol 44 (3) ◽  
pp. 321-341 ◽  
Author(s):  
P. J. Avery
Keyword(s):  
Population Genetics ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Disease Genes ◽  
Effective Population ◽  
Random Drift ◽  
Mutation Pressure ◽  
Electrophoretic Data ◽  
Fitness Parameters

SUMMARYFrom the available electrophoretic data, it is clear that haplodiploid insects have a much lower level of genetic variability than diploid insects, a difference that is only partially explained by the social structure of some haplodiploid species. The data comparing X-linked genes and autosomal genes in the same species is much more sparse and little can be inferred from it. This data is compared with theoretical analyses of X-linked genes and genes in haplodiploids. (The theoretical population genetics of X-linked genes and genes in haplodiploids are identical.) X-linked genes under directional selection will be lost or fixed more quickly than autosomal genes as selection acts more directly on X-linked genes and the effective population size is smaller. However, deleterious disease genes, maintained by mutation pressure, will give higher disease incidences at X-linked loci and hence rare mutants are easier to detect at X-linked loci. Considering the forces which can maintain balanced polymorphisms, there are much stronger restrictions on the fitness parameters at X-linked loci than at autosomal loci if genetic variability is to be maintained, and thus fewer polymorphic loci are to be expected on the X-chromosome and in haplodiploids. However, the mutation-random drift hypothesis also leads to the expectation of lower heterozygosity due to the decrease in effective population size. Thus the theoretical results fit in with the data but it is still subject to argument whether selection or mutation-random drift are maintaining most of the genetic variability at X-linked genes and genes in haplodiploids.

scholarly journals Repeatability of adaptation in experimental populations of different sizes

2015 ◽  
Vol 282 (1805) ◽  
pp. 20143033 ◽  
Author(s):  
Josianne Lachapelle ◽  
Joshua Reid ◽  
Nick Colegrave
Keyword(s):  
Population Size ◽  
Large Contribution ◽  
Unicellular Alga ◽  
Effective Population ◽  
Fitness Level ◽  
Relative Contribution ◽  
Large Populations ◽  
Population Sizes ◽  
Evolutionary Trajectories ◽  
Experimental Populations

The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine which component of evolution is affected by population size. We find that adaptation to salt is repeatable at the fitness level in medium ( N e = 5 × 10 4 ) and large ( N e = 4 × 10 5 ) populations because of the large contribution of selection. Adaptation is not repeatable in small ( N e = 5 × 10 3 ) populations because of large constraints from history. The threshold between stochastic and deterministic evolution in this case is therefore between effective population sizes of 10 3 and 10 4 . Our results indicate that diversity across populations is more likely to be maintained if they are small. Experimental outcomes in large populations are likely to be robust and can inform our predictions about outcomes in similar situations.

scholarly journals Protein Evolution Depends on Multiple Distinct Population Size Parameters

2017 ◽  
Author(s):  
Alexander Platt ◽  
Claudia C Weber ◽  
David A Liberles
Keyword(s):  
Population Size ◽  
Protein Evolution ◽  
Functional Constraints ◽  
Effective Population ◽  
Coding Sequences ◽  
The Many ◽  
Definition Of ◽  
Evolution Of Proteins ◽  
The Relationship ◽  
New Mutations

AbstractThat population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distinct roles for population size that characterize different processes should affect the evolution of proteins and need to be carefully defined. Empirical evidence is consistent with a role for demography in influencing protein evolution, supporting the idea that functional constraints alone do not determine the composition of coding sequences.Given that the relationship between population size, mutant fitness and fixation probability has been well characterized, estimating fitness from observed substitutions is well within reach with well-formulated models. Molecular evolution research has, therefore, increasingly begun to leverage concepts from population genetics to quantify the selective effects associated with different classes of mutation. However, in order for this type of analysis to provide meaningful information about the intra- and inter-specific evolution of coding sequences, a clear definition of concepts of population size, what they influence, and how they are best parameterized is essential.Here, we present an overview of the many distinct concepts that “population size” and “effective population size” may refer to, what they represent for studying proteins, and how this knowledge can be harnessed to produce better specified models of protein evolution.

scholarly journals THE INBREEDING EFFECTIVE POPULATION NUMBER AND THE EXPECTED HOMOZYGOSITY FOR AN X-LINKED LOCUS

Genetics ◽  
1981 ◽  
Vol 97 (3-4) ◽  
pp. 731-737
Author(s):  
Thomas Nagylaki
Keyword(s):  
Genetic Variability ◽  
Joint Action ◽  
Random Mating ◽  
Effective Population ◽  
Random Drift ◽  
Population Number ◽  
Asymptotic Rate ◽  
Large Populations

ABSTRACT Assuming random mating and discrete nonoverlapping generations, the inbreeding effective population number, N(i)  e, is calculated for an X-linked locus. For large populations, the result agrees with the variance effective population number. As an application, the maintenance of genetic variability by the joint action of mutation and random drift is investigated. It is shown that, if every allele mutates at rate u to new types, then the probabilities of identity in state (and hence the expected homozygosity of females) converge to the approximate value (1 + 4N(i)  eu)-1 at the approximate asymptotic rate exp{—[2u + (2N(i)e)-1]t}.

The Genetic Effective Size of a Population

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Structure ◽  
Population Subdivision ◽  
Effective Population ◽  
Entire Genome ◽  
History Of ◽  
A Site ◽  
The Hill ◽  
New Mutations

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.

scholarly journals Population size influences the type of nucleotide variations in humans

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
High Frequency ◽  
Genetic Diseases ◽  
Large Population ◽  
Low Frequency ◽  
Small Population ◽  
Effective Population ◽  
Genome Data ◽  
Large Populations

Abstract Background It is well known that the effective size of a population (Ne) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes. Results Our results revealed that for low frequency variants, the ratio of AT→GC to GC→AT variants (β) was similar across populations, suggesting the similarity of the pattern of mutation in various populations. However, for high frequency variants, β showed a positive correlation with the effective population size of the populations. This suggests a much higher proportion of high frequency AT→GC variants in large populations (e.g. Africans) compared to those with small population sizes (e.g. Asians). These results imply that the substitution patterns vary significantly between populations. These findings could be explained by the effect of GC-biased gene conversion (gBGC), which favors the fixation of G/C over A/T variants in populations. In large population, gBGC causes high β. However, in small populations, genetic drift reduces the effect of gBGC resulting in reduced β. This was further confirmed by a positive relationship between Ne and β for homozygous variants. Conclusions Our results highlight the huge variation in the types of homozygous and high frequency polymorphisms between world populations. We observed the same pattern for deleterious variants, implying that the homozygous polymorphisms associated with recessive genetic diseases will be more enriched with G or C in populations with large Ne (e.g. Africans) than in populations with small Ne (e.g. Europeans).

scholarly journals The effect of population size on effective population size: an empirical study in the red flour beetle Tribolium castaneum

1996 ◽  
Vol 68 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Leslie A. Pray ◽  
Charles J. Goodnight ◽  
Lori Stevens ◽  
James M. Schwartz ◽  
Guiyun Yan
Keyword(s):  
Population Size ◽  
Tribolium Castaneum ◽  
Evolutionary Biology ◽  
Negative Relationship ◽  
Red Flour Beetle ◽  
Published Data ◽  
Effective Population ◽  
Flour Beetle ◽  
Large Populations ◽  
Population Sizes

SummaryDespite the increasing number of studies on the magnitude of Ne/N ratios, much remains unknown about the effects of demographic and environmental variables on Ne/N. We determined Ne/N for seven population size treatments, ranging from N = 2 to N = 960, in the red flour beetle Tribolium castaneum. Ne/N decreased with increasing N, as evidenced by a significant negative relationship between log N and Ne/N. Our results are consistent with other published data on the relationship between Ne/N and N. Effective population sizes in large populations may be much smaller than previously recognized. These results have important implications for conservation and evolutionary biology.

scholarly journals Management of genetic diversity using gene dropping method based on pedigree information

2013 ◽  
Vol 56 (1) ◽  
pp. 518-526
Author(s):  
M. Khaldari ◽  
A. N. Javaremi ◽  
A. Pakdel ◽  
H. M. Yeganeh ◽  
P. Berg
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Low Frequency ◽  
Pedigree Analysis ◽  
Simulation Software ◽  
Pedigree Information ◽  
Genetic Contribution ◽  
Effective Population ◽  
Management Plans

Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.

scholarly journals Predictable county-level estimates of R0 for COVID-19 needed for public health planning in the USA

2020 ◽  
Author(s):  
Anthony R. Ives ◽  
Claudio Bozzuto
Keyword(s):  
Public Health ◽  
Population Density ◽  
Population Size ◽  
Communicable Disease ◽  
Health Planning ◽  
Spatial Location ◽  
County Level ◽  
Rate Of Spread ◽  
Geographical Regions ◽  
The Usa

The basic reproduction number, R0, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Estimated R0 values are only useful, however, if they accurately predict the future potential rate of spread. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA. Among-county variance in the rate of spread was explained by four factors: the timing of the county-level outbreak, population size, population density, and spatial location. Of these, the effect of timing is explained by early steps that people and governments took to reduce transmission, and population size is explained by the sample size of deaths that affects the statistical ability to estimate R0. For predictions of future spread, population density is important, likely because it scales the average contact rate among people, while spatial location can be explained by differences in the transmissibility of SARS-CoV-2 strains in different geographical regions of the USA. The high predictability of R0 based on population density and spatial location allowed us to extend estimates to all 3109 counties in the lower 48 States. The high variation of R0 among counties argues for public health policies that are enacted at the county level for controlling COVID-19.

Sign in / Sign up

Export Citation Format

Share Document