Krause, J., Unger, T., Nocon, A., Malaspinas, A-S., Kolokotronis, S-O., Stiller, M., ...
© 2008 Krause et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),...
Krause, J., Unger, T., Nocon, A., Malaspinas, A-S., Kolokotronis, S-O., Stiller, M., ...
© 2008 Krause et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),...
Neff, Mark W, Robertson, K R, Wong, A K, Safra, N, Broman, K W, Slatkin, M, ...
A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of...
Mutational processes of simple-sequence repeat loci in human populations.
Di Rienzo, A, Peterson, A C, Garza, J C, Valdes, A M, Slatkin, M, Freimer, N B
Mutational processes of simple sequence repeats (SSRs) in complex genomes are poorly understood. We examined these processes by introducing a two-phase mutation model. In this model, most mutations...
Lenski, R E, Slatkin, M, Ayala, F J
Bacterial populations have served as model systems for studying evolutionary processes ever since the classic experiments of Luria and Delbrück, which demonstrated the occurrence of mutations prior...
To account for the transmission of mitochondrial DNA between conspecific species Drosophila pseudoobscura and D. persimilis in sympatry reported by J.R. Powell [Powell, J.R. (1983) Proc. Natl. Acad....
Coevolution in structured demes.
A simple model of coevolution in a subdivided population is considered. It is shown that, when there are frequency- and density-dependent interactions in each site, the sampling variation in numbers...
Group selection on a quantitative character
We derive a model of group and individual selection on a quantitative character that is similar to the single-locus “metapopulation” models of group selection. Two alternative methods for the...
Incorporating genotypes of relatives into a test of linkage disequilibrium.
Genetic data from autosomal loci in diploids generally consist of genotype data for which no phase information is available, making it difficult to implement a test of linkage disequilibrium. In this...
Likelihood analysis of disequilibrium mapping, and related problems.
In this paper a theory is developed that provides the sampling distribution of alleles at a diallelic marker locus closely linked to a low-frequency allele that arose as a single mutant. The sampling...
Disequilibrium mapping of a quantitative-trait locus in an expanding population.
Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of...
Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution
Seperack, P., Slatkin, M., Arnheim, N.
Members of the rDNA multigene family within a species do not evolve independently, rather, they evolve together in a concerted fashion. Between species, however, each multigene family does evolve...
Detecting Small Amounts of Gene Flow from Phylogenies of Alleles
The method of coalescents is used to find the probability that none of the ancestors of alleles sampled from a population are immigrants. If that is the case for samples from two or more populations,...
A Cladistic Measure of Gene Flow Inferred from the Phylogenies of Alleles
A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is...
The Quantitative Genetic Consequences of Pleiotropy under Stabilizing and Directional Selection
The independence of two phenotypic characters affected by both pleiotropic and nonpleiotropic mutations is investigated using a generalization of M. Slatkin's stepwise mutation model of 1987. The...
Detecting Isolation by Distance Using Phylogenies of Genes
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events...
F(st) in a Hierarchical Island Model
It is shown that in a hierarchical island model, in which demes within a neighborhood exchange migrants at a much higher rate than do demes in different neighborhoods, hierarchical F statistics...
Pairwise Comparisons of Mitochondrial DNA Sequences in Stable and Exponentially Growing Populations
We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population...
Estimation of Levels of Gene Flow from DNA Sequence Data
Hudson, R. R., Slatkin, M., Maddison, W. P.
We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating F(ST) from frequencies at polymorphic sites, treating...
Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited
Valdes, A. M., Slatkin, M., Freimer, N. B.
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...
Linkage Disequilibrium in Growing and Stable Populations
Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant...
Gene and Allelic Genealogies at a Gametophytic Self-Incompatibility Locus
The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is...
Gene Genealogies within Mutant Allelic Classes
A coalescent theory of the gene genealogy within an allelic class that arises by a unique mutational event is developed and analyzed. To interpret this theory it was necessary to expand on existing...
The Sampling Distribution of Disease-Associated Alleles
A theory is developed that provides the sampling distribution of low frequency alleles at a single locus under the assumption that each allele is the result of a unique mutation. The numbers of...
Using maximum likelihood to estimate population size from temporal changes in allele frequencies.
We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the...
Overdominant alleles in a population of variable size.
An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection...
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...
A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with...
The use of intraallelic variability for testing neutrality and estimating population growth rate.
To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely...
Genetic drift in sex-linked lethal disorders.
Slatkin, M, Thomson, G, Sawyer, S
A model is considered to calculate effects of genetic drift on the expected proportion of new mutants amongst males affected by a sex-linked recessive lethal. We show how to relate the number of...
Mutational processes of simple-sequence repeat loci in human populations.
Di Rienzo, A, Peterson, A C, Garza, J C, Valdes, A M, Slatkin, M, Freimer, N B
Mutational processes of simple sequence repeats (SSRs) in complex genomes are poorly understood. We examined these processes by introducing a two-phase mutation model. In this model, most mutations...
Lenski, R E, Slatkin, M, Ayala, F J
Bacterial populations have served as model systems for studying evolutionary processes ever since the classic experiments of Luria and Delbrück, which demonstrated the occurrence of mutations prior...
To account for the transmission of mitochondrial DNA between conspecific species Drosophila pseudoobscura and D. persimilis in sympatry reported by J.R. Powell [Powell, J.R. (1983) Proc. Natl. Acad....
Coevolution in structured demes.
A simple model of coevolution in a subdivided population is considered. It is shown that, when there are frequency- and density-dependent interactions in each site, the sampling variation in numbers...
Group selection on a quantitative character
We derive a model of group and individual selection on a quantitative character that is similar to the single-locus “metapopulation” models of group selection. Two alternative methods for the...
Linkage Disequilibrium in Human Ribosomal Genes: Implications for Multigene Family Evolution
Seperack, P., Slatkin, M., Arnheim, N.
Members of the rDNA multigene family within a species do not evolve independently, rather, they evolve together in a concerted fashion. Between species, however, each multigene family does evolve...
Detecting Small Amounts of Gene Flow from Phylogenies of Alleles
The method of coalescents is used to find the probability that none of the ancestors of alleles sampled from a population are immigrants. If that is the case for samples from two or more populations,...
A Cladistic Measure of Gene Flow Inferred from the Phylogenies of Alleles
A method for estimating the average level of gene flow among populations is introduced. The method provides an estimate of Nm, where N is the size of each local population in an island model and m is...
The Quantitative Genetic Consequences of Pleiotropy under Stabilizing and Directional Selection
The independence of two phenotypic characters affected by both pleiotropic and nonpleiotropic mutations is investigated using a generalization of M. Slatkin's stepwise mutation model of 1987. The...
Detecting Isolation by Distance Using Phylogenies of Genes
We introduce a method for analyzing phylogenies of genes sampled from a geographically structured population. A parsimony method can be used to compute s, the minimum number of migration events...
F(st) in a Hierarchical Island Model
It is shown that in a hierarchical island model, in which demes within a neighborhood exchange migrants at a much higher rate than do demes in different neighborhoods, hierarchical F statistics...
Pairwise Comparisons of Mitochondrial DNA Sequences in Stable and Exponentially Growing Populations
We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population...
Estimation of Levels of Gene Flow from DNA Sequence Data
Hudson, R. R., Slatkin, M., Maddison, W. P.
We compare the utility of two methods for estimating the average levels of gene flow from DNA sequence data. One method is based on estimating F(ST) from frequencies at polymorphic sites, treating...
Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited
Valdes, A. M., Slatkin, M., Freimer, N. B.
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...
Linkage Disequilibrium in Growing and Stable Populations
Nonrandom associations between alleles at different loci can be tested for using Fisher's exact test. Extensive simulations show that there is a substantial probability of obtaining significant...
Gene and Allelic Genealogies at a Gametophytic Self-Incompatibility Locus
The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is...
Gene Genealogies within Mutant Allelic Classes
A coalescent theory of the gene genealogy within an allelic class that arises by a unique mutational event is developed and analyzed. To interpret this theory it was necessary to expand on existing...
The Sampling Distribution of Disease-Associated Alleles
A theory is developed that provides the sampling distribution of low frequency alleles at a single locus under the assumption that each allele is the result of a unique mutation. The numbers of...
Incorporating genotypes of relatives into a test of linkage disequilibrium.
Genetic data from autosomal loci in diploids generally consist of genotype data for which no phase information is available, making it difficult to implement a test of linkage disequilibrium. In this...
Likelihood analysis of disequilibrium mapping, and related problems.
In this paper a theory is developed that provides the sampling distribution of alleles at a diallelic marker locus closely linked to a low-frequency allele that arose as a single mutant. The sampling...
Disequilibrium mapping of a quantitative-trait locus in an expanding population.
Linkage disequilibrium (LD) mapping can be successful if there is strong nonrandom association between marker alleles and an allele affecting a trait of interest. The principles of LD mapping of...
Using maximum likelihood to estimate population size from temporal changes in allele frequencies.
We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the...
Overdominant alleles in a population of variable size.
An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection...
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...
A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with...
The use of intraallelic variability for testing neutrality and estimating population growth rate.
To better understand the forces affecting individual alleles, we introduce a method for finding the joint distribution of the frequency of a neutral allele and the extent of variability at closely...
Genetic drift in sex-linked lethal disorders.
Slatkin, M, Thomson, G, Sawyer, S
A model is considered to calculate effects of genetic drift on the expected proportion of new mutants amongst males affected by a sex-linked recessive lethal. We show how to relate the number of...
Estimating the age of alleles by use of intraallelic variability.
A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in...
Allele age and a test for selection on rare alleles.
An approximate expression for the probability distribution of the age of a neutral allele as a function of its frequency is derived for a population undergoing arbitrary changes in population size. A...