Infinite Allele Mutation Model Research Articles

Genetic analysis of microsatellite polymorphism in the Elliot's Pheasant (Syrmaticus ellioti) in China

In this study, we reported the population genetic analyses in the Elliot's Pheasant(Syrnaticus ellioti) using seven polymorphism microsatellite loci based on 105 individuals from 4 geographical populations. Departures from Hardy-Weinberg equilibrium were found in four geographical populations. The average number of alleles was 8.86, with a total of 62 alleles across 7 loci; observed heterozygosity (HO) was generally low and the average number was 0.504. For the seven microsatellite loci, the polymorphism information content ranged from 0.549 to 0.860, with an average number 0.712. Population bottlenecks of the four geographical populations were tested by infinite allele mutation model, step-wise mutation model and two-phase mutation model, which found that each population had experienced bottleneck effect during the recent period. Fst analysis across all geographical populations indicated that the genetic differentiaton between the Guizhou geographical population and the Hunan geographical population was highly significant (P<0.001), a finding supported by the far genetic relationship showed by the neighbor-joining tree of four geographical populations based on Nei's unbiased genetic distances. Using hierarchical analysis of molecular variance (Guizhou geographical population relative to all others pooled), we found a low level of the genetic variation among geographical populations and that between groups. However, differences among populations relative to the total sample explained most of the genetic variance (92.84%), which was significant.

An asymptotic sampling formula for the coalescent with Recombination

Ewens sampling formula (ESF) is a one-parameter family of probability distributions with a number of intriguing combinatorial connections. This elegant closed-form formula first arose in biology as the stationary probability distribution of a sample configuration at one locus under the infinite-alleles model of mutation. Since its discovery in the early 1970s, the ESF has been used in various biological applications, and has sparked several interesting mathematical generalizations. In the population genetics community, extending the underlying random-mating model to include recombination has received much attention in the past, but no general closed-form sampling formula is currently known even for the simplest extension, that is, a model with two loci. In this paper, we show that it is possible to obtain useful closed-form results in the case the population-scaled recombination rate ρ is large but not necessarily infinite. Specifically, we consider an asymptotic expansion of the two-locus sampling formula in inverse powers of ρ and obtain closed-form expressions for the first few terms in the expansion. Our asymptotic sampling formula applies to arbitrary sample sizes and configurations.

Contrasting microsatellite variation between subalpine and western larch, two closely related species with different distribution patterns

Subalpine larch (Larix lyallii Parl.) and western larch (Larix occidentalis Nutt.) represent two closely related species with contrasting abundance and distribution patterns in Western North America. Genetic diversity at seven informative microsatellite loci was determined for 19 populations of subalpine larch and nine populations of western larch. Contrasting genetic diversity and patterns of population differentiation were observed between the two species. The overall within-population genetic diversity parameters were lower in subalpine larch (A = 3.2; A(P) = 3.6; H(E) = 0.418) than in western larch (A(P) = 5.51; H(E) = 0.580), a pattern that is likely related to historical or demographic factors. No evidence of interspecific hybridization was observed. Significantly more population differentiation (theta = 0.15; R(ST) = 0.07), consistent with more restricted gene flow, was observed for subalpine larch as compared to western larch (theta = 0.05; R(ST) = 0.04). Under the assumption of an infinite allele mutation model, 12 of the 19 subalpine larch populations showed signs of deviation from the mutation-drift equilibrium, which suggests Holocene population bottlenecks and fluctuations in effective population size for this species. None of the western larch populations deviated significantly from the mutation-drift equilibrium. For both species, Mantel's test revealed a significant positive relationship between geographical and genetic distances indicative of isolation by distance. A similar geographical structure was detected in both species, suggesting at least two genetically distinct glacial populations in each species. The various implications for gene conservation are discussed.

Genetic variability and population structure of dorada ( Brycon moorei sinuensis Dahl) in the Sinú River, Córdoba, Colombia

Six microsatellite loci, isolated for Piaractus mesopotamicus (Characidae, Serrasalminae) were used to evaluate the genetic variability of the dorada (Brycon moorei sinuensis, Characidae, Bryconinae) population in the Sinú River, Córdoba, Colombia, and to facilitate management recommendations for this species. The six loci were polymorphic, with an average of 9.25 alleles for dimeric loci (Pme2, Pme4, Pme5 and Pme20), and five alleles for trimeric loci. Tests for linkage disequilibrium were used to determine that the six loci had an independent distribution. The observed heterozygosities were lower than the expected ones for all loci, and the population was not in Hardy–Weinberg equilibrium because of heterozygote deficiency. F-statistics indicated inbreeding and a low population substructure. The homogeneity of the population was confirmed by high values of genetic flux and an agglomerated representation of the individuals, based on factor correspondence analysis. Recent bottlenecks were detected for three sample sites under the assumption of an infinite allele mutation model. Proposals for the management of the dorada population are made and validated with a genetic simulation.

Balancing selection at closely linked, overdominant loci in a finite population.

High levels of allelic diversity and strong linkage disequilibrium are found in the major histocompatibility (MHC) system in humans and other vertebrates. This article proposes several descriptive statistics that quantify the extent and pattern of strong linkage disequilibrium between pairs of highly polymorphic loci. It also develops an approximate analytic theory incorporating the effects of balancing selection, mutation, recombination, and genetic drift at two closely linked loci and compares the theoretical predictions with published surveys of the MHC class II loci, DQA1 and DQB1, in humans and nonhuman primates. The descriptive statistics proposed include the fraction of complementary haplotypes (haplotypes with D' = 1), the fraction of excess haplotypes, and the numbers of alleles at each locus in complementary haplotypes with one or more alleles at the other locus. The model assumes the infinite alleles model of mutation and the symmetric overdominance model of selection. Analytic approximations in some cases are obtained in the strong selection, weak mutation (SSWM) limit introduced by J. Gillespie. The predictions of the approximate analysis are confirmed by simulation. Both the analytic theory and simulations show that relatively few haplotypes will be found when selection is strong and recombination is weak relative to genetic drift. The model can reproduce many of the observed patterns at DQA1 and DQB1 provided that the recombination rate is assumed to be very small.

MUTATION, A MICROCOMPUTER MODULE DESIGNED FOR PLANT BREEDING AND GENETICS

A teaching module was developed for computer-aided instruction of mutation theory. The Hypercard-driven, Macintosh compatible module illustrates the concepts of: 1) Changes in allele frequency with mutation pressure; 2) Number of alleles maintained in populations, and; 3) The Neutrality Hypothesis. The concepts are integrated in an application by using a game format.Mutation is the ultimate source of genetic variation. Mutation pressure results in changes in allele frequency. Concept 1 illustrates the theoretical changes in allele frequency under pressure of reversible mutation. Mutation equilibrium is depicted as P=V/u+v; where v=mutation rates of allele A and u of allele a. The Infinite-Alleles Model of mutation is illustrated in Concept 2 and specifies characteristics of new mutations by F=1/4Nu+1, where F=fixation index and N=number in population. Concept 3 demonstrates the hypothesis that polymorphisms result from selectively neutral alleles maintained in a balance between mutation and random genetic drift.

MUTATION, A MICROCOMPUTER MODULE DESIGNED FOR PLANT BREEDING AND GENETICS

A teaching module was developed for computer-aided instruction of mutation theory. The Hypercard-driven, Macintosh compatible module illustrates the concepts of: 1) Changes in allele frequency with mutation pressure; 2) Number of alleles maintained in populations, and; 3) The Neutrality Hypothesis. The concepts are integrated in an application by using a game format. Mutation is the ultimate source of genetic variation. Mutation pressure results in changes in allele frequency. Concept 1 illustrates the theoretical changes in allele frequency under pressure of reversible mutation. Mutation equilibrium is depicted as P=V/u+v; where v=mutation rates of allele A and u of allele a. The Infinite-Alleles Model of mutation is illustrated in Concept 2 and specifies characteristics of new mutations by F=1/4Nu+1, where F=fixation index and N=number in population. Concept 3 demonstrates the hypothesis that polymorphisms result from selectively neutral alleles maintained in a balance between mutation and random genetic drift.