Conservation Genetics

, Volume 11, Issue 6, pp 2425–2430

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

  • Phillip R. England
  • Gordon Luikart
  • Robin S. Waples
Short Communication

DOI: 10.1007/s10592-010-0112-x

Cite this article as:
England, P.R., Luikart, G. & Waples, R.S. Conserv Genet (2010) 11: 2425. doi:10.1007/s10592-010-0112-x


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 Ne 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 Ne = 1,000 into demes of Ne = 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 Ne-reduction signal is still apparent in the presence of considerable migration (m ~ 0.10–0.25). Single-sample genetic estimates of Ne thus show considerable promise for early detection of population fragmentation and decline.


Ne Effective population size Linkage disequilibrium Fragmentation Bottleneck Connectivity Monitoring Conservation 

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Phillip R. England
    • 1
  • 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

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