Infinite-allele model and infinite-site model in population genetics

1996 ◽  
Vol 75 (1) ◽  
pp. 27-31 ◽  
Author(s):  
Fumio Tajima
Keyword(s):  
Population Genetics ◽  
Infinite Allele Model ◽  
Site Model ◽  
Infinite Site Model ◽  
Allele Model

scholarly journals THE EFFECT OF INTRAGENIC RECOMBINATION ON THE NUMBER OF ALLELES IN A FINITE POPULATION

Genetics ◽  
1978 ◽  
Vol 88 (4) ◽  
pp. 829-844 ◽  
Author(s):  
Curtis Strobeck ◽  
Kenneth Morgan
Keyword(s):  
Finite Population ◽  
Natural Populations ◽  
Intragenic Recombination ◽  
Infinite Allele Model ◽  
Site Model ◽  
Significant Process ◽  
Mean And Variance ◽  
The Mean ◽  
Allele Model ◽  
Size Data

ABSTRACT A two-site infinite allele model is constructed to study the effect of intragenic recombination on the number of neutral alleles and the distribution of their frequencies in a finite population. The results of theory and Monte Carlo simulation of the two-site model demonstrate that intragenic recombination significantly increases the mean and variance of the number of alleles when the rates of mutation and recombination are as large as the reciprocal of the population size. Data from natural populations indicate that this may be a significant process in generating variation and determining its distribution.

scholarly journals Equilibrium Values of Measures of Population Subdivision for Stepwise Mutation Processes

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1357-1362
Author(s):  
François Rousset
Keyword(s):  
Population Structure ◽  
Population Subdivision ◽  
Identity By Descent ◽  
Infinite Allele Model ◽  
Coalescence Time ◽  
Stepwise Mutation ◽  
Expected Values ◽  
The Relationship ◽  
Allele Model ◽  
Coalescence Times

Abstract Expected values of Wright'sF-statistics are functions of probabilities of identity in state. These values may be quite different under an infinite allele model and under stepwise mutation processes such as those occurring at microsatellite loci. However, a relationship between the probability of identity in state in stepwise mutation models and the distribution of coalescence times can be deduced from the relationship between probabilities of identity by descent and the distribution of coalescence times. The values of FIS and FST can be computed using this property. Examination of the conditional probability of identity in state given some coalescence time and of the distribution of coalescence times are also useful for explaining the properties of FIS and FST at high mutation rate loci, as shown here in an island model of population structure.

scholarly journals Infinite allele model with varying mutation rate.

1976 ◽  
Vol 73 (11) ◽  
pp. 4164-4168 ◽  
Author(s):  
M. Nei ◽  
R. Chakraborty ◽  
P. A. Fuerst
Keyword(s):  
Mutation Rate ◽  
Infinite Allele Model ◽  
Allele Model

scholarly journals Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 679-695 ◽  
Author(s):  
A Estoup ◽  
L Garnery ◽  
M Solignac ◽  
J M Cornuet
Keyword(s):  
Apis Mellifera ◽  
Phylogenetic Trees ◽  
Microsatellite Data ◽  
Effective Population ◽  
Average Heterozygosity ◽  
Microsatellite Variation ◽  
Infinite Allele Model ◽  
Population Sizes ◽  
Stepwise Mutation ◽  
Allele Model

Abstract Samples from nine populations belonging to three African (intermissa, scutellata and capensis) and four European (mellifera, ligustica, carnica and cecropia) Apis mellifera subspecies were scored for seven microsatellite loci. A large amount of genetic variation (between seven and 30 alleles per locus) was detected. Average heterozygosity and average number of alleles were significantly higher in African than in European subspecies, in agreement with larger effective population sizes in Africa. Microsatellite analyses confirmed that A. mellifera evolved in three distinct and deeply differentiated lineages previously detected by morphological and mitochondrial DNA studies. Dendrogram analysis of workers from a given population indicated that super-sisters cluster together when using a sufficient number of microsatellite data whereas half-sisters do not. An index of classification was derived to summarize the clustering of different taxonomic levels in large phylogenetic trees based on individual genotypes. Finally, individual population x loci data were used to test the adequacy of the two alternative mutation models, the infinite allele model (IAM) and the stepwise mutation models. The better fit overall of the IAM probably results from the majority of the microsatellites used including repeats of two or three different length motifs (compound microsatellites).

scholarly journals THE SAMPLING DISTRIBUTION OF LINKAGE DISEQUILIBRIUM

Genetics ◽  
1984 ◽  
Vol 108 (1) ◽  
pp. 257-274 ◽  
Author(s):  
G B Golding
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Correlation Coefficient ◽  
Bimodal Distribution ◽  
Test Statistic ◽  
Effective Population ◽  
Chi Square ◽  
Infinite Allele Model ◽  
Allele Model

ABSTRACT The probabilities of obtaining particular samples of gametes with two completely linked loci are derived. It is assumed that the population consists of N diploid, randomly mating individuals, that each of the two loci mutate according to the infinite allele model at a rate µ and that the population is at equilibrium. When 4Nµ is small, the most probable samples of gametes are those that segregate only two alleles at either locus. The probabilities of various samples of gametes are discussed. The results show that most samples with completely linked loci have either a very small or a very large association between the alleles of each locus. This causes the distribution of linkage disequilibrium to be skewed and the distribution of the correlation coefficient to be bimodal. The correlation coefficient is commonly used as a test statistic with a chi square distribution and yet has a bimodal distribution when the loci are completely linked. Thus, such a test is not likely to be accurate unless the rate of recombination between the loci and/or the effective population size are sufficiently large enough so that the loci can be treated as unlinked.

scholarly journals Twenty-five years ago in genetics: the infinite allele model.

Genetics ◽  
1989 ◽  
Vol 121 (4) ◽  
pp. 631-634
Author(s):  
J F Crow
Keyword(s):  
Infinite Allele Model ◽  
Allele Model

scholarly journals Neutrality tests based on the distribution of haplotypes under an infinite-site model

1998 ◽  
Vol 15 (12) ◽  
pp. 1788-1790 ◽  
Author(s):  
F. Depaulis ◽  
M. Veuille
Keyword(s):  
Site Model ◽  
Infinite Site Model ◽  
Neutrality Tests

scholarly journals The Amount of DNA Polymorphism Maintained in a Finite Population When the Neutral Mutation Rate Varies Among Sites

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1457-1465 ◽  
Author(s):  
Fumio Tajima
Keyword(s):  
Mutation Rate ◽  
Finite Population ◽  
Rate Variation ◽  
Effective Population ◽  
Site Model ◽  
New Methods ◽  
Infinite Site Model ◽  
Minimum Number ◽  
Input Model ◽  
Neutral Mutation Rate

Abstract The expectations of the average number of nucleotide differences per site (π), the proportion of segregating site (s), the minimum number of mutations per site (s*) and some other quantities were derived under the finite site models with and without rate variation among sites, where the finite site models include Jukes and Cantor's model, the equal-input model and Kimura's model. As a model of rate variation, the gamma distribution was used. The results indicate that if distribution parameter α is small, the effect of rate variation on these quantities are substantial, so that the estimates of θ based on the infinite site model are substantially underestimated, where θ = 4Nv, N is the effective population size and vis the mutation rate per site per generation. New methods for estimating θ are also presented, which are based on the finite site models with and without rate variation. Using these methods, underestimation can be corrected.

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