LIKELIHOOD ANALYSIS OF ONGOING GENE FLOW AND HISTORICAL ASSOCIATION

@inproceedings{Nielsen2000LIKELIHOODAO,
  title={LIKELIHOOD ANALYSIS OF ONGOING GENE FLOW AND HISTORICAL ASSOCIATION},
  author={Rasmus Nielsen and Montgomery Slatkin},
  booktitle={Evolution; international journal of organic evolution},
  year={2000}
}
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… 
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58 Citations
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58 Citations

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.

Divergence between human populations estimated from linkage disequilibrium.

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.

An approximate likelihood for genetic data under a model with recombination and population splitting.

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.

PERSPECTIVE: GENE DIVERGENCE, POPULATION DIVERGENCE, AND THE VARIANCE IN COALESCENCE TIME IN PHYLOGEOGRAPHIC STUDIES

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.
...

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