Skip to main content
Log in

Comparison of methods for detecting bottlenecks from microsatellite loci

  • Published:
Conservation Genetics Aims and scope Submit manuscript


This paper describes simulation tests to compare methods for detecting recent bottlenecks using microsatellite data. This study considers both type I error (detecting a bottleneck when there wasn’t one) and type II error (failing to detect a bottleneck when there was one) under a variety of scenarios. The two most promising methods were the range in allele size conditioned on the number of alleles, M k , and heterozygosity given the number of alleles, H k , under a two-phase mutation model; in most of the simulations one of these two methods had the lowest type I and type II error relative to other methods. M k was the method most likely to correctly identify a bottleneck when a bottleneck lasted several generations, the population had made a demographic recovery, and mutation rates were high or pre-bottleneck population sizes were large. On the other hand H k was most likely to correctly identify a bottleneck when a bottleneck was more recent and less severe and when mutation rates were low or pre-bottleneck population sizes were small. Both methods were prone to type I errors when assumptions of the model were violated, but it may be easier to design a conservative heterozygosity test than a conservative ratio test.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others


  • Anderson E.C., Williamson E.G., Thompson E.A. (2000) Monte carlo evaluation of the likelihood for N e from temporally spaced samples. Genetics 156:2109–2118

    PubMed  CAS  Google Scholar 

  • Beaumont M.A. (1999) Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029

    PubMed  CAS  Google Scholar 

  • Cornuet J.M., Luikart G. (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014

    PubMed  CAS  Google Scholar 

  • Di Rienzo A., Peterson A.C., Garza J.C., Valdes A.M., Slatkin M., Freimer N.B. (1994) Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91:3166–3170

    Article  PubMed  CAS  Google Scholar 

  • Ewens W.J. (1979). Mathematical Population Genetics. Springer-Verlag, New York

    Google Scholar 

  • Frankham R. (1995) Conservation genetics. Annu Rev Genet 29:305–327

    Article  PubMed  CAS  Google Scholar 

  • Frankham R. (1999) Quantitative genetics in conservation biology. Genet Res 74:237–244

    Article  PubMed  CAS  Google Scholar 

  • Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol. Ecol., 305–318

  • Lande R. (1994) Risk of population extinction from fixation of new deleterious mutations. Evolution 48:1460–1469

    Article  Google Scholar 

  • Luikart G.L., Allendof F.W., Cornuet J.M., Sherwin W.B. (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89:238–247

    Article  PubMed  CAS  Google Scholar 

  • Newman D., Pilson D. (1997) Increased probability of extinction due to decreased genetic effective population size: experimental population of Clarkia pulchella. Evolution 51:345–362

    Article  Google Scholar 

  • Piry S., Luikart G., Cornuet J.M. (1999) BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity 90:502–503

    Article  Google Scholar 

  • Schwartz M.K., Tallmon D.A., Luikart G. (1998) Review of DNA-based census and effective population size estimators. Animal Conservation 1:293–299

    Article  Google Scholar 

  • Tavare S. (1984) Line-of-descent and genealogical processes, and their applications in population genetics models. Theoretical Population Biology 26:119–164

    Article  PubMed  CAS  Google Scholar 

  • Waples R.S. (1989) A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121:379–391

    PubMed  CAS  Google Scholar 

  • Williamson E.G., Slatkin M. (1999) Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics 152:755–761

    PubMed  CAS  Google Scholar 

Download references


This study was supported by NIH grant GM40282 to M. Slatkin. I would like to thank J.C. Garza, C. Muirhead, R.D. Schnabel, M. Slatkin, and T.J. Ward for many helpful comments and suggestions.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Ellen G. Williamson-Natesan.



The transition between an equilibrium population to a bottlenecked population required the transition from a coalescent simulation to a full Wright–Fisher simulation. To do this, I generated a sample of size 2N b using the coalescent simulation. This sample represented the entire population during the first generation of the bottleneck.

Simulating the recovery from a bottleneck to a large population size required the transition from the full Wright–Fisher simulation to the coalescent simulation. This transition was more complicated because coalescent simulations keep track of only the sample and ancestors of the sample backward in time while full Wright–Fisher simulations require information on the entire population and work forward in time. First, using the size of the sample and the time since the bottleneck as input parameters, I used a coalescent simulation to determine the number of ancestors, n, of the sample, that were present immediately after recovery from the bottleneck. Thus, the coalescent simulation of the recovered population was stopped after a specific amount of time, T, unlike the pre-bottleneck simulation, which was stopped when all lineages coalesced to a single common ancestor. Allele sizes of these n ancestors were then determined by sampling (with replacement) n individuals from the bottlenecked population (the last generation of the full Wright–Fisher simulation). Finally, allele sizes for the sample from the recovered population were determined by the mutations and coalescent events dictated by the coalescent simulation that determined n.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Williamson-Natesan, E.G. Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv Genet 6, 551–562 (2005).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: