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.

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 Haplogroup-specific deviation from the stepwise mutation model at the microsatellite loci DYS388 and DYS392

2001 ◽  
Vol 9 (1) ◽  
pp. 22-26 ◽  
Author(s):  
Almut Nebel ◽  
Dvora Filon ◽  
Carsten Hohoff ◽  
Marina Faerman ◽  
Bernd Brinkmann ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Stepwise Mutation Model ◽  
Mutation Model ◽  
Stepwise Mutation

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 Dynamics of Microsatellite Divergence Under Stepwise Mutation and Proportional Slippage/Point Mutation Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 839-852 ◽  
Author(s):  
Peter P Calabrese ◽  
Richard T Durrett ◽  
Charles F Aquadro
Keyword(s):  
Point Mutations ◽  
Genetic Distances ◽  
Mutational Bias ◽  
Human Populations ◽  
Mutation Model ◽  
Perfect Repeat ◽  
Stepwise Mutation ◽  
Equilibrium Distributions ◽  
Theoretical Results ◽  
Polymerase Slippage

Abstract Recently Kruglyak, Durrett, Schug, and Aquadro showed that microsatellite equilibrium distributions can result from a balance between polymerase slippage and point mutations. Here, we introduce an elaboration of their model that keeps track of all parts of a perfect repeat and a simplification that ignores point mutations. We develop a detailed mathematical theory for these models that exhibits properties of microsatellite distributions, such as positive skewness of allele lengths, that are consistent with data but are inconsistent with the predictions of the stepwise mutation model. We use our theoretical results to analyze the successes and failures of the genetic distances (δμ)2 and DSW when used to date four divergences: African vs. non-African human populations, humans vs. chimpanzees, Drosophila melanogaster vs. D. simulans, and sheep vs. cattle. The influence of point mutations explains some of the problems with the last two examples, as does the fact that these genetic distances have large stochastic variance. However, we find that these two features are not enough to explain the problems of dating the human-chimpanzee split. One possible explanation of this phenomenon is that long microsatellites have a mutational bias that favors contractions over expansions.

An Analysis of Microsatellite Loci in Arabidopsis thaliana: Mutational Dynamics and Application

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1475-1488
Author(s):  
V Vaughan Symonds ◽  
Alan M Lloyd
Keyword(s):  
Arabidopsis Thaliana ◽  
Microsatellite Loci ◽  
Current Knowledge ◽  
Flowering Plant ◽  
Allele Frequency Distribution ◽  
Strongly Correlated ◽  
Microsatellite Evolution ◽  
Stepwise Mutation ◽  
Mutation Pattern ◽  
Infinite Alleles Model

Abstract Microsatellite loci are among the most commonly used molecular markers. These loci typically exhibit variation for allele frequency distribution within a species. However, the factors contributing to this variation are not well understood. To expand on the current knowledge of microsatellite evolution, 20 microsatellite loci were examined for 126 accessions of the flowering plant, Arabidopsis thaliana. Substantial variability in mutation pattern among loci was found, most of which cannot be explained by the assumptions of the traditional stepwise mutation model or infinite alleles model. Here it is shown that the degree of locus diversity is strongly correlated with the number of contiguous repeats, more so than with the total number of repeats. These findings support a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Results of cluster analyses are also presented, demonstrating the potential of microsatellite loci for resolving relationships among accessions of A. thaliana.

scholarly journals Microsatellite evolution in sunfish (Centrarchidae)

1999 ◽  
Vol 56 (7) ◽  
pp. 1198-1205 ◽  
Author(s):  
Bryan D Neff ◽  
Peng Fu ◽  
Mart R Gross
Keyword(s):  
Microsatellite Loci ◽  
Micropterus Salmoides ◽  
Lepomis Macrochirus ◽  
Sequence Divergence ◽  
Mendelian Inheritance ◽  
Lepomis Gibbosus ◽  
Microsatellite Evolution ◽  
Stepwise Mutation ◽  
Flanking Sequences ◽  
Infinite Alleles Model

We describe 10 microsatellite loci from bluegill (Lepomis macrochirus) and discuss their evolution within the Centrarchidae. All of the loci exhibit Mendelian inheritance and are unlinked. While six loci are conserved within the Centrarchidae (found also in pumpkinseed (Lepomis gibbosus) and largemouth bass (Micropterus salmoides)), four have origins outside the family and two predate it by 65-150 million years. The persistence of these loci in fish may be due to a slow rate of sequence divergence within their flanking sequences, estimated at 0.14-0.83% per million years. We examine the number of alleles, heterozygosity, range, modes, and the frequency of the most common allele and find that a two-phased model (TPM) or an infinite alleles-model (IAM) best describes the results, while a stepwise mutation model (SMM) is rejected. Therefore, population differentiation analyses utilizing these microsatellite loci should consider parameters based on the IAM (e.g., FST) and not the SMM.

scholarly journals THE STEPWISE MUTATION MODEL: AN EXPERIMENTAL EVALUATION UTILIZING HEMOGLOBIN VARIANTS

Genetics ◽  
1980 ◽  
Vol 94 (1) ◽  
pp. 185-201
Author(s):  
Paul A Fuerst ◽  
Robert E Ferrell
Keyword(s):  
Amino Acid ◽  
Electrophoretic Mobility ◽  
Tertiary Structure ◽  
Stepwise Mutation Model ◽  
Starch Gel Electrophoresis ◽  
Human Hemoglobin ◽  
Net Charge ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
Hemoglobin Variants

ABSTRACT The stepwise mutation model of OHTA and KIMURA (1973) was proposed to explain patterns of genetic variability revealed by means of electrophoresis. The assumption that electrophoretic mobility was principally determined by unit changes in net molecular charge has been criticized by JOHNSON (1974, 1977). This assumption has been tested directly using hemoglobin. Twenty-seven human hemoglobin variants with known amino acid substitutions, and 26 nonhuman hemoglobins with known sequences were studied by starch gel electrophoresis. Of these hemoglobin% 60 to 70% had electrophoretic mobilities that could be predicted solely on the basis of net charge calculated from the amino acid composition alone, ignoring tertiary structure. Only four hemoglobins showed a mobility that was clearly different from an expected mobility calculated using only the net charge of the molecule. For the remaining 30% of hemoglobins studied, mobility was determined by a combination. of net charge and other unidentified components, probably reflecting changes in ionization of some amino acid residues as a result of small alterations in tertiary structure due to the amino acid substitution in the variant. For the nonhuman hemoglobins, the deviation of a sample from its expected mobility increased with increasing amino acid divergence from human hemoglobin A.—It is concluded that the net electrostatic charge of a molecule is the principal determinant of electrophoretic mobility under the conditions studied. However, because of the significant deviation from strict stepwise mobility detected for 30 to 40% of the variants studied, it is further concluded that the infinite-allele model of KIMURA and CROW (1964) or a "mixed model" such as that proposed by LI (1976) may be more appropriate than the stepwise mutation model for the analysis of much of the available electrophoretic data from natural populations.

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