Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Dec 2000; 156(4): 2109–2118.
PMCID: PMC1461352

Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples.


A population's effective size is an important quantity for conservation and management. The effective size may be estimated from the change of allele frequencies observed in temporally spaced genetic samples taken from the population. Though moment-based estimators exist, recently Williamson and Slatkin demonstrated the advantages of a maximum-likelihood approach that they applied to data on diallelic genetic markers. Their computational methods, however, do not extend to data on multiallelic markers, because in such cases exact evaluation of the likelihood is impossible, requiring an intractable sum over latent variables. We present a Monte Carlo approach to compute the likelihood with data on multiallelic markers. So as to be computationally efficient, our approach relies on an importance-sampling distribution constructed by a forward-backward method. We describe the Monte Carlo formulation and the importance-sampling function and then demonstrate their use on both simulated and real datasets.

Full Text

The Full Text of this article is available as a PDF (315K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Jorde PE, Ryman N. Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics. 1995 Feb;139(2):1077–1090. [PMC free article] [PubMed]
  • Nei M, Tajima F. Genetic drift and estimation of effective population size. Genetics. 1981 Jul;98(3):625–640. [PMC free article] [PubMed]
  • Pollak E. A new method for estimating the effective population size from allele frequency changes. Genetics. 1983 Jul;104(3):531–548. [PMC free article] [PubMed]
  • Waples RS. A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics. 1989 Feb;121(2):379–391. [PMC free article] [PubMed]
  • Williamson EG, Slatkin M. Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics. 1999 Jun;152(2):755–761. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...