scholarly journals Estimating the Total Number of Alleles Using a Sample Coverage Method

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1365-1373 ◽  
Author(s):  
Shu-Pang Huang ◽  
B S Weir
Keyword(s):  
Recurrent Mutation ◽  
Allele Frequencies ◽  
Simulation Studies ◽  
Infinite Allele Model ◽  
Mutation Model ◽  
True Number ◽  
Stepwise Mutation ◽  
Microsatellite Alleles ◽  
Allele Model

Abstract Previously reported methods for estimating the number of different alleles at a single locus in a population have not described a useful general result. Using the number of alleles observed in a sample gives an underestimate for the true number of alleles. The similar problem of estimating the number of species in a population was first investigated in 1943. In this article we use the sample coverage method proposed by Chao and Lee in 1992 to estimate the number of alleles in a population when there are unequal allele frequencies. Simulation studies under the recurrent mutation model show that, for reasonable sample sizes, a significantly better estimate of the true number can be obtained than that using only the observed alleles. Results under the stepwise mutation model and infinite-allele model are presented. Possible applications include improving the characterization of the prior distribution for the allele frequencies, adjusting the estimates of genetic diversity, and estimating the range of microsatellite alleles.

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 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 Mutation at the Human D1S80 Minisatellite Locus

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Kuppareddi Balamurugan ◽  
Martin L. Tracey ◽  
Uwe Heine ◽  
George C. Maha ◽  
George T. Duncan
Keyword(s):  
Mutation Rate ◽  
Chromosome 1 ◽  
Infinite Allele Model ◽  
Minisatellite Locus ◽  
Repeat Array ◽  
Mutation Model ◽  
Close Proximity ◽  
Stepwise Mutation ◽  
One Step ◽  
The One

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of1.04×10-4and a female mutation rate of5.18×10-5with an overall mutation rate of approximately7.77×10-5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

scholarly journals A measure of population subdivision based on microsatellite allele frequencies.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 457-462 ◽  
Author(s):  
M Slatkin
Keyword(s):  
Microsatellite Loci ◽  
Allele Frequencies ◽  
Stepwise Mutation Model ◽  
Population Subdivision ◽  
Population Divergence ◽  
Migration Rates ◽  
Mutation Model ◽  
Subdivided Populations ◽  
Stepwise Mutation ◽  
Unbiased Estimates

Abstract A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].

scholarly journals A MIXED MODEL OF MUTATION FOR ELECTROPHORETIC IDENTITY OF PROTEINS WITHIN AND BETWEEN POPULATIONS

Genetics ◽  
1976 ◽  
Vol 83 (2) ◽  
pp. 423-432
Author(s):  
Wen-Hsiung Li
Keyword(s):  
Genetic Distance ◽  
Mixed Model ◽  
Present Model ◽  
Natural Populations ◽  
The Other ◽  
Effective Number ◽  
Infinite Allele Model ◽  
Stepwise Mutation ◽  
Allele Model ◽  
Nei's Genetic Distance

ABSTRACT A model which is a mixture of the model of infinite alleles and the Ohta-Kimura model of stepwise mutation has been proposed for the study of eletcrophoretic variants in natural populations. Mutations which alter the mobility of a protein are divided into two classes: stepwise mutations and nonstepwise mutations. It is assumed that stepwise mutations follow the Ohta-Kimura model while nonstepwise mutations follow the infinite allele model. It is then shown that even if the proportion of nonstepwise mutations is only 5%, with the other 95% stepwise mutations, the effective number of alleles given by the present model is considerably larger than that given by the Ohta-Kimura model of stepwise mutation. The result has also been applied to study Nei's genetic distance.

Signatures of Population Expansion in Microsatellite Repeat Data

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1921-1930 ◽  
Author(s):  
Marek Kimmel ◽  
Ranajit Chakraborty ◽  
J Patrick King ◽  
Michael Bamshad ◽  
W Scott Watkins ◽  
...  
Keyword(s):  
Population Expansion ◽  
Logistic Growth ◽  
Racial Groups ◽  
Equilibrium Conditions ◽  
Allele Size ◽  
Infinite Allele Model ◽  
Moran Model ◽  
Tetranucleotide Repeats ◽  
Stepwise Mutation ◽  
Allele Model

Abstract To examine the signature of population expansion on genetic variability at microsatellite loci, we consider a population that evolves according to the time-continuous Moran model, with growing population size and mutations that follow a general asymmetric stepwise mutation model. We present calculations of expected allele-size variance and homozygosity at a locus in such a model for several variants of growth, including stepwise, exponential, and logistic growth. These calculations in particular prove that population bottleneck followed by growth in size causes an imbalance between allele size variance and heterozygosity, characterized by the variance being transiently higher than expected under equilibrium conditions. This effect is, in a sense, analogous to that demonstrated before for the infinite allele model, where the number of alleles transiently increases after a stepwise growth of population. We analyze a set of data on tetranucleotide repeats that reveals the imbalance expected under the assumption of bottleneck followed by population growth in two out of three major racial groups. The imbalance is strongest in Asians, intermediate in Europeans, and absent in Africans. This finding is consistent with previous findings by others concerning the population expansion of modern humans, with the bottleneck event being most ancient in Africans, most recent in Asians, and intermediate in Europeans. Nevertheless, the imbalance index alone cannot reliably estimate the time of initiation of population expansion.

scholarly journals THE SAMPLING DISTRIBUTION OF LINKAGE DISEQUILIBRIUM UNDER AN INFINITE ALLELE MODEL WITHOUT SELECTION

Genetics ◽  
1985 ◽  
Vol 109 (3) ◽  
pp. 611-631
Author(s):  
Richard R Hudson
Keyword(s):  
Linkage Disequilibrium ◽  
Joint Distribution ◽  
High Linkage Disequilibrium ◽  
Allele Frequencies ◽  
Sufficient Information ◽  
Neutral Model ◽  
Infinite Allele Model ◽  
Sampling Distributions ◽  
The Mean ◽  
Allele Model

ABSTRACT The sampling distributions of several statistics that measure the association of alleles on gametes (linkage disequilibrium) are estimated under a two-locus neutral infinite allele model using an efficient Monte Carlo method. An often used approximation for the mean squared linkage disequilibrium is shown to be inaccurate unless the proper statistical conditioning is used. The joint distribution of linkage disequilibrium and the allele frequencies in the sample is studied. This estimated joint distribution is sufficient for obtaining an approximate maximum likelihood estimate of C = 4Nc, where N is the population size and c is the recombination rate. It has been suggested that observations of high linkage disequilibrium might be a good basis for rejecting a neutral model in favor of a model in which natural selection maintains genetic variation. It is found that a single sample of chromosomes, examined at two loci cannot provide sufficient information for such a test if C < 10, because with C this small, very high levels of linkage disequilibrium are not unexpected under the neutral model. In samples of size 50, it is found that, even when C is as large as 50, the distribution of linkage disequilibrium conditional on the allele frequencies is substantially different from the distribution when there is no linkage between the loci. When conditioned on the number of alleles at each locus in the sample, all of the sample statistics examined are nearly independent of λ = 4Nμ, where μ is the neutral mutation rate.

scholarly journals New Methods Employing Multilocus Genotypes to Select or Exclude Populations as Origins of Individuals

Genetics ◽  
1999 ◽  
Vol 153 (4) ◽  
pp. 1989-2000 ◽  
Author(s):  
Jean-Marie Cornuet ◽  
Sylvain Piry ◽  
Gordon Luikart ◽  
Arnaud Estoup ◽  
Michel Solignac
Keyword(s):  
Genetic Distance ◽  
Bayesian Method ◽  
Simulated Data ◽  
Unknown Origin ◽  
Infinite Allele Model ◽  
Multilocus Genotypes ◽  
Mutation Model ◽  
Distance Methods ◽  
Stepwise Mutation ◽  
Time Of Divergence

Abstract A new method for assigning individuals of unknown origin to populations, based on the genetic distance between individuals and populations, was compared to two existing methods based on the likelihood of multilocus genotypes. The distribution of the assignment criterion (genetic distance or genotype likelihood) for individuals of a given population was used to define the probability that an individual belongs to the population. Using this definition, it becomes possible to exclude a population as the origin of an individual, a useful extension of the currently available assignment methods. Using simulated data based on the coalescent process, the different methods were evaluated, varying the time of divergence of populations, the mutation model, the sample size, and the number of loci. Likelihood-based methods (especially the Bayesian method) always performed better than distance methods. Other things being equal, genetic markers were always more efficient when evolving under the infinite allele model than under the stepwise mutation model, even for equal values of the differentiation parameter Fst. Using the Bayesian method, a 100% correct assignment rate can be achieved by scoring ca. 10 microsatellite loci (H ≈ 0.6) on 30–50 individuals from each of 10 populations when the Fst is near 0.1.

scholarly journals Allele frequencies at microsatellite loci: the stepwise mutation model revisited.

Genetics ◽  
1993 ◽  
Vol 133 (3) ◽  
pp. 737-749 ◽  
Author(s):  
A M Valdes ◽  
M Slatkin ◽  
N B Freimer
Keyword(s):  
Mutation Rate ◽  
Microsatellite Loci ◽  
Allele Frequencies ◽  
Stepwise Mutation Model ◽  
Human Populations ◽  
Effective Population ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation

Abstract We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.

scholarly journals An evaluation of genetic distances for use with microsatellite loci.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 463-471 ◽  
Author(s):  
D B Goldstein ◽  
A Ruiz Linares ◽  
L L Cavalli-Sforza ◽  
M W Feldman
Keyword(s):  
Microsatellite Loci ◽  
Phylogenetic Reconstruction ◽  
Genetic Distances ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
The Difference ◽  
Nei's Distance ◽  
Infinite Alleles Model ◽  
Overall Reliability

Abstract Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.

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