author={Rasmus Nielsen and Montgomery Slatkin},
  booktitle={Evolution; international journal of organic evolution},
Abstract We develop a Monte Carlo–based likelihood method for estimating migration rates and population divergence times from data at unlinked loci at which mutation rates are sufficiently low that, in the recent past, the effects of mutation can be ignored. The method is applicable to restriction fragment length polymorphisms (RFLPs) and single nucleotide polymorphisms (SNPs) sampled from a subdivided population. The method produces joint maximum-likelihood estimates of the migration rate and… 

Distinguishing migration from isolation: a Markov chain Monte Carlo approach.

The results show that even a single nonrecombining genetic locus can provide substantial power to test the hypothesis of no ongoing migration and/or to test models of symmetric migration between the two populations.

Interpretation of variation across marker loci as evidence of selection.

It is found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus, and the conditional distribution is less sensitive to the values of nuisance parameters.

Population divergence time estimation using individual lineage label switching

A new Bayes inference method is presented that treats the divergence time as a random variable, calculated from an assembly of splitting events on individual lineages in a genealogy, which allows easy integration into the standard coalescence framework used in programs such as MIGRATE.

Stochastic Models and Statistical Inference In Evolutionary Genetics: Using DNA Sequence Data To Learn About Population Divergence And Speciation

A maximum-likelihood estimation method is developed which is appropriate for data sets containing observations from many independent loci, and is both very efficient and able to deal with mutation rate heterogeneity, and a simulation method to estimate the limiting distribution of the likelihood ratio statistic when the true parameter vector lies on the boundary of the parameter space is developed.

Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis

A Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters is applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis, with considerable variation in gene flow estimates among loci, in both directions between the species.

Beyond FST: Analysis of population genetic data for conservation

A guide to recently developed methods for population genetic analysis, including identification of population structure, quantification of gene flow, and inference of demographic history, with a special focus on methods relevant to conservation genetic applications.


It is shown that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial.

Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach

  • P. BeerliJ. Felsenstein
  • Mathematics
    Proceedings of the National Academy of Sciences of the United States of America
  • 2001
A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed and used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.



Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.

A new method for the estimation of migration rates and effective population sizes is described, which uses a maximum-likelihood framework based on coalescence theory and is as good as or better than those from an optimized FST-based measure.


The maximum‐likelihood estimator provides a statistical framework for the analysis of population history given genetic data and is compared to a commonly applied estimator based on Wright's FST statistic.

Inference from gene trees in a subdivided population.

This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the

Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum.

This paper shows how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that is due to historical events.

Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model.

  • R. Nielsen
  • Mathematics
    Theoretical population biology
  • 1998
In this paper, a maximum likelihood estimator of population divergence time based on the infinite sites model is developed. It is demonstrated how this estimator may be applied to obtain maximum

Estimation in an island model using simulation.

Estimation for an island model where mutation maintains a k-allele neutral polymorphism at a single locus on each island is considered and an estimate of variance of the estimate of the migration parameter is obtained using the likelihood trajectory.

Mitochondrial and nuclear genes present conflicting portraits of human origins.

  • J. Hey
  • Biology
    Molecular biology and evolution
  • 1997
The discrepancy in the mtDNA-nuclear difference suggests that mitochondrial variation has been shaped by natural selection, and may not be ideal for some questions on human origins.

Segregating sites in Wright's island model.

  • J. Wakeley
  • Mathematics
    Theoretical population biology
  • 1998
A new estimator of the population migration rate is proposed and is shown to outperform the widely used pairwise method and hold quite well for the finite-island model in many cases.

Distinguishing migration from isolation using the variance of pairwise differences.

  • J. Wakeley
  • Computer Science
    Theoretical population biology
  • 1996
The variance of the number of differences between pairs of sequences in a single sample is studied and forms the basis of a test of the isolation model, one possible alternative to isolation.

RFLP analysis on a sample from northern Italy.

A sample of 55 unrelated individuals from Trino Vercellese, a village in northern Italy, represents the only European sample which is unmixed in a comparative study of eight populations from four continents, and genetic variability between populations was measured.