scholarly journals Coalescence theory for a general class of structured populations with fast migration

2011 ◽  
Vol 43 (04) ◽  
pp. 1027-1047 ◽  
Author(s):  
O. Hössjer
Keyword(s):  
Population Size ◽  
General Class ◽  
Population Genetic ◽  
Total Population ◽  
Structured Populations ◽  
Effective Population ◽  
Constant Change ◽  
Skorokhod Topology ◽  
Age Structured ◽  
Dependency Structures

In this paper we study a general class of population genetic models where the total population is divided into a number of subpopulations or types. Migration between subpopulations is fast. Extending the results of Nordborg and Krone (2002) and Sagitov and Jagers (2005), we prove, as the total population sizeNtends to ∞, weak convergence of the joint ancestry of a given sample of haploid individuals in the Skorokhod topology towards Kingman's coalescent with a constant change of time scalec. Our framework includes age-structured models, geographically structured models, and combinations thereof. We also allow each individual to have offspring in several subpopulations, with general dependency structures between the number of offspring of various types. As a byproduct, explicit expressions for the coalescent effective population sizeN/care obtained.

scholarly journals Coalescence theory for a general class of structured populations with fast migration

2011 ◽  
Vol 43 (4) ◽  
pp. 1027-1047 ◽  
Author(s):  
O. Hössjer
Keyword(s):  
Population Size ◽  
General Class ◽  
Population Genetic ◽  
Total Population ◽  
Structured Populations ◽  
Effective Population ◽  
Constant Change ◽  
Skorokhod Topology ◽  
Age Structured ◽  
Dependency Structures

In this paper we study a general class of population genetic models where the total population is divided into a number of subpopulations or types. Migration between subpopulations is fast. Extending the results of Nordborg and Krone (2002) and Sagitov and Jagers (2005), we prove, as the total population size N tends to ∞, weak convergence of the joint ancestry of a given sample of haploid individuals in the Skorokhod topology towards Kingman's coalescent with a constant change of time scale c. Our framework includes age-structured models, geographically structured models, and combinations thereof. We also allow each individual to have offspring in several subpopulations, with general dependency structures between the number of offspring of various types. As a byproduct, explicit expressions for the coalescent effective population size N/c are obtained.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

scholarly journals In with the Old, in with the New: The Promiscuity of the Duplication Process Engenders Diverse Pathways for Novel Gene Creation

2012 ◽  
Vol 2012 ◽  
pp. 1-24 ◽  
Author(s):  
Vaishali Katju
Keyword(s):  
Gene Duplication ◽  
Population Size ◽  
Population Genetic ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Dna And Rna ◽  
Duplication Events ◽  
History Of ◽  
Theoretical Population ◽  
Novel Exon

The gene duplication process has exhibited far greater promiscuity in the creation of paralogs with novel exon-intron structures than anticipated even by Ohno. In this paper I explore the history of the field, from the neo-Darwinian synthesis through Ohno’s formulation of the canonical model for the evolution of gene duplicates and culminating in the present genomic era. I delineate the major tenets of Ohno’s model and discuss its failure to encapsulate the full complexity of the duplication process as revealed in the era of genomics. I discuss the diverse classes of paralogs originating from both DNA- and RNA-mediated duplication events and their evolutionary potential for assuming radically altered functions, as well as the degree to which they can function unconstrained from the pressure of gene conversion. Lastly, I explore theoretical population-genetic considerations of how the effective population size (Ne) of a species may influence the probability of emergence of genes with radically altered functions.

scholarly journals Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine (Pinus strobus): Conservation Value and Climate Adaptation Potential

2021 ◽  
Vol 12 ◽  
Author(s):  
Om P. Rajora ◽  
John W. R. Zinck
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Conservation Value ◽  
Adaptive Potential ◽  
Effective Population ◽  
White Pine ◽  
Old Growth ◽  
Second Growth

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

The broad-snouted caiman population recovery in Argentina. A case of genetics conservation

2017 ◽  
Vol 38 (4) ◽  
pp. 411-424 ◽  
Author(s):  
Patricia Susana Amavet ◽  
Eva Carolina Rueda ◽  
Juan César Vilardi ◽  
Pablo Siroski ◽  
Alejandro Larriera ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Population Recovery ◽  
Santa Fe ◽  
Effective Population ◽  
Population Genetic Parameters ◽  
The Impact

Caiman latirostriswild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure ofC. latirostrispopulations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.

scholarly journals Stochastic Interplay between Mutation and Recombination during the Acquisition of Drug Resistance Mutations in Human Immunodeficiency Virus Type 1

2005 ◽  
Vol 79 (21) ◽  
pp. 13572-13578 ◽  
Author(s):  
Christian L. Althaus ◽  
Sebastian Bonhoeffer
Keyword(s):  
Human Immunodeficiency Virus ◽  
Drug Resistance ◽  
Population Size ◽  
Mutation Rate ◽  
Population Genetic ◽  
Resistance Mutations ◽  
Effective Population ◽  
Drug Resistance Mutations ◽  
Immunodeficiency Virus ◽  
Population Sizes

ABSTRACT The emergence of drug resistance mutations in human immunodeficiency virus (HIV) has been a major setback in the treatment of infected patients. Besides the high mutation rate, recombination has been conjectured to have an important impact on the emergence of drug resistance. Population genetic theory suggests that in populations limited in size recombination may facilitate the acquisition of beneficial mutations. The viral population in an infected patient may indeed represent such a population limited in size, since current estimates of the effective population size range from 500 to 105. To address the effects of limited population size, we therefore expand a previously described deterministic population genetic model of HIV replication by incorporating the stochastic processes that occur in finite populations of infected cells. Using parameter estimates from the literature, we simulate the evolution of drug-resistant viral strains. The simulations show that recombination has only a minor effect on the rate of acquisition of drug resistance mutations in populations with effective population sizes as small as 1,000, since in these populations, viral strains typically fix beneficial mutations sequentially. However, for intermediate effective population sizes (104 to 105), recombination can accelerate the evolution of drug resistance by up to 25%. Furthermore, a reduction in population size caused by drug therapy can be overcome by a higher viral mutation rate, leading to a faster evolution of drug resistance.

Evaluation of a method for maintaining age-structured populations of house-flies, Musca domestica L. (Diptera: Muscidae), to study the evolution of insecticide resistance

1986 ◽  
Vol 76 (2) ◽  
pp. 297-302 ◽  
Author(s):  
I. Denholm ◽  
R. M. Sawicki ◽  
A. W. Farnham ◽  
Jean C. White
Keyword(s):  
Insecticide Resistance ◽  
Population Size ◽  
Musca Domestica ◽  
Regression Line ◽  
Structured Populations ◽  
Equilibrium Density ◽  
Independent Manner ◽  
House Flies ◽  
Age Structured ◽  
Insecticide Control

AbstractAn inexpensive and versatile method for maintaining age-structured Musca domestica L. populations for studies on the evolution of insecticide resistance is described. Adult flies are kept in spacious aluminium cages in which age-structuring is maintained by the thrice-weekly addition of pupae bred from eggs collected from within the cages. The population size is regulated in a density-independent manner by constraining the input of pupae to that necessary to maintain the required equilibrium density of adults within a cage. Adult numbers are monitored by photographing from outside the cage flies settled on a grid etched on the rear wall, and by converting this grid count to an estimate of population size using a calculated regression line. Observed changes in fly numbers in a cage accorded well with those predicted by a computer model using empirical data on larval productivity, and the emergence and survivorship schedules of adult flies. Since a variety of insecticide control regimes can be applied within the cage, this system enables an adequate yet tractable simulation of selection for resistance by insecticides under field conditions.

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