Conservation Genetics

, Volume 11, Issue 6, pp 2425–2430 | Cite as

Early detection of population fragmentation using linkage disequilibrium estimation of effective population size

  • Phillip R. EnglandEmail author
  • Gordon Luikart
  • Robin S. Waples
Short Communication


Population subdivision due to habitat loss and modification, exploitation of wild populations and altered spatial population dynamics is of increasing concern in nature. Detecting population fragmentation is therefore crucial for conservation management. Using computer simulations, we show that a single sample estimator of N e based on linkage disequilibrium is a highly sensitive and promising indicator of recent population fragmentation and bottlenecks, even with some continued gene flow. For example, fragmentation of a panmictic population of N e = 1,000 into demes of N e = 100 can be detected with high probability after a single generation when estimates from this method are compared to prefragmentation estimates, given data for ~20 microsatellite loci in samples of 50 individuals. We consider a range of loci (10–40) and individuals (25–100) typical of current studies of natural populations and show that increasing the number of loci gives nearly the same increase in precision as increasing the number of individuals sampled. We also evaluated effects of incomplete fragmentation and found this N e-reduction signal is still apparent in the presence of considerable migration (m ~ 0.10–0.25). Single-sample genetic estimates of N e thus show considerable promise for early detection of population fragmentation and decline.


Ne Effective population size Linkage disequilibrium Fragmentation Bottleneck Connectivity Monitoring Conservation 



PRE was assisted by an Australian Academy of Sciences Visit to North America Fellowship. GL was partially supported by a grant to FLBS from the Walton Family Foundation and by the Portuguese-American Foundation for Development, CIBIO, and UP. We thank Fred Allendorf for discussions and hosting the visit to his lab by PRE.


  1. Allendorf FW, Luikart G (2006) Conservation and the genetics of populations. Wiley Blackwell, OxfordGoogle Scholar
  2. Balloux F (2001) EasyPop (version 1.7): a computer program for population genetics simulations. J Hered 92:301–302CrossRefPubMedGoogle Scholar
  3. Cornuet J-M, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014PubMedGoogle Scholar
  4. England PR, Cornuet J-M, Berthier P, Tallmon DA, Luikart G (2006) Estimating effective population size from linkage disequilibrium: severe bias using small samples. Conserv Genet 7:303–308CrossRefGoogle Scholar
  5. Estoup A, Angers B (1998) Microsatellites and minisatellites for molecular ecology. In: Carvalho G (ed) Advances in molecular ecology. IOS Press, Amsterdam, pp 55–86Google Scholar
  6. Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140CrossRefGoogle Scholar
  7. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, CambridgeGoogle Scholar
  8. Hill WG (1981) Estimation of effective population size from data on linkage disequilibrium. Genet Res Camb 38:209–216CrossRefGoogle Scholar
  9. Leberg P (2005) Genetic approaches for estimating the effective size of populations. J Wildl Manag 69:1385–1399CrossRefGoogle Scholar
  10. Luikart G, Cornuet J-M, Allendorf FW (1999) Temporal changes in allele frequencies provide estimates of population bottleneck size. Conserv Biol 13:523–530CrossRefGoogle Scholar
  11. Nei M, Li W-H (1973) Linkage disequilibrium in subdivided populations. Genetics 75:213–219PubMedGoogle Scholar
  12. Nomura T (2008) Estimation of effective number of breeders from molecular coancestry of single cohort sample. Evol Appl 1:462–474CrossRefGoogle Scholar
  13. Ovenden JR, Peel D, Street R, Courtney AJ, Hoyle SD, Peel S, Podlich H (2007) The genetic effective and adult census sixe of an Australian population of tiger prawns (Penaeus esculentus). Mol Ecol 16:127–138CrossRefPubMedGoogle Scholar
  14. Schwartz MK, Tallmon DA, Luikart G (1998) Review of DNA-based census and effective population size estimators. Anim Conserv 1:293–299CrossRefGoogle Scholar
  15. Tallmon DA, Koyuk A, Luikart G, Beaumont MA (2008) OneSamp: a program to estimate effective population size using approximate Bayesian computation. Mol Ecol Resour 8:299–301CrossRefGoogle Scholar
  16. Vitalis R, Couvet D (2001) Estimation of effective population size and migration rate 22 from one- and two-locus identity measures. Genetics 157:911–925PubMedGoogle Scholar
  17. Wang J (2005) Estimation of effective population sizes from data on genetic markers. Philos Trans R Soc B 360:1395–1409CrossRefGoogle Scholar
  18. Wang J (2009) A new method for estimating effective population size from a single sample of multilocus genotypes. Mol Ecol 18:2148–2164CrossRefPubMedGoogle Scholar
  19. Waples RS (2005) Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Mol Ecol 14:3335–3352CrossRefPubMedGoogle Scholar
  20. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv Genet 7(2):167–184CrossRefGoogle Scholar
  21. Waples RS, Do C (2008) L d N e: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8:753–756CrossRefGoogle Scholar
  22. Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary N e using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol Appl 3:244–262CrossRefGoogle Scholar
  23. Weir BS (1979) Inferences about linkage disequilibrium. Biometrics 35:235–254CrossRefPubMedGoogle Scholar
  24. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159PubMedGoogle Scholar
  25. Young AG, Clark GM (eds) (2000) Genetics demography and viability of fragmented populations. Cambridge University Press, EnglandGoogle Scholar
  26. Zartman CE, McDaniel SF, Shaw J (2006) Experimental habitat fragmentation increases linkage disequilibrium but does not affect genetic diversity or population structure in the Amazonian liverwort Radula flaccida. Mol Ecol 15:2305–2315CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Phillip R. England
    • 1
    Email author
  • Gordon Luikart
    • 2
    • 3
  • Robin S. Waples
    • 4
  1. 1.CSIRO Marine and Atmospheric Research and Wealth from Oceans FlagshipHobartAustralia
  2. 2.Flathead Lake Biological Station (FLBS)University of MontanaPolsonUSA
  3. 3.Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), Universidade do PortoVairãoPortugal
  4. 4.NOAA FisheriesNorthwest Fisheries Science CentreSeattleUSA

Personalised recommendations