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Genetics. Jan 2003; 163(1): 429–446.
PMCID: PMC1462406

Estimating effective population size and migration rates from genetic samples over space and time.

Abstract

In the past, moment and likelihood methods have been developed to estimate the effective population size (N(e)) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of N(e) if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N(e) and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N(e), respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N(e) and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

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Selected References

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  • The International Psoriasis Genetics Study: assessing linkage to 14 candidate susceptibility loci in a cohort of 942 affected sib pairs. Am J Hum Genet. 2003 Aug;73(2):430–437. [PMC free article] [PubMed]
  • Anderson EC, Williamson EG, Thompson EA. Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples. Genetics. 2000 Dec;156(4):2109–2118. [PMC free article] [PubMed]
  • Beaumont MA. Detecting population expansion and decline using microsatellites. Genetics. 1999 Dec;153(4):2013–2029. [PMC free article] [PubMed]
  • Beerli P, Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4563–4568. [PMC free article] [PubMed]
  • Caballero A. Developments in the prediction of effective population size. Heredity (Edinb) 1994 Dec;73(Pt 6):657–679. [PubMed]
  • Tajima F, Nei M. Note on genetic drift and estimation of effective population size. Genetics. 1984 Mar;106(3):569–574. [PMC free article] [PubMed]
  • Vitalis R, Couvet D. Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics. 2001 Feb;157(2):911–925. [PMC free article] [PubMed]
  • Wang J. A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet Res. 2001 Dec;78(3):243–257. [PubMed]
  • Wang J. Optimal marker-assisted selection to increase the effective size of small populations. Genetics. 2001 Feb;157(2):867–874. [PMC free article] [PubMed]
  • Funk WC, Tallmon DA, Allendorf FW. Small effective population size in the long-toed salamander. Mol Ecol. 1999 Oct;8(10):1633–1640. [PubMed]
  • Whitlock MC, McCauley DE. Indirect measures of gene flow and migration: FST not equal to 1/(4Nm + 1). Heredity (Edinb) 1999 Feb;82(Pt 2):117–125. [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]
  • Jehle R, Arntzen JW, Burke T, Krupa AP, Hödl W. The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus). Mol Ecol. 2001 Apr;10(4):839–850. [PubMed]
  • Wright S. Evolution in Mendelian Populations. Genetics. 1931 Mar;16(2):97–159. [PMC free article] [PubMed]
  • Jehle R, Arntzen JW, Burke T, Krupa AP, Hödl W. The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus). Mol Ecol. 2001 Apr;10(4):839–850. [PubMed]
  • Kantanen J, Olsaker I, Adalsteinsson S, Sandberg K, Eythorsdottir E, Pirhonen K, Holm LE. Temporal changes in genetic variation of north European cattle breeds. Anim Genet. 1999 Feb;30(1):16–27. [PubMed]
  • Luikart G, Cornuet JM. Estimating the effective number of breeders from heterozygote excess in progeny. Genetics. 1999 Mar;151(3):1211–1216. [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]
  • Nielsen R, Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics. 2001 Jun;158(2):885–896. [PMC free article] [PubMed]
  • Pamilo P, Varvio-Aho SL. On the estimation of population size from allele frequency changes. Genetics. 1980 Aug;95(4):1055–1057. [PMC free article] [PubMed]
  • Pudovkin AI, Zaykin DV, Hedgecock D. On the potential for estimating the effective number of breeders from heterozygote-excess in progeny. Genetics. 1996 Sep;144(1):383–387. [PMC free article] [PubMed]
  • Rannala B, Mountain JL. Detecting immigration by using multilocus genotypes. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9197–9201. [PMC free article] [PubMed]

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