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

Phillip R. England, Gordon Luikart, Robin S. Waples

Research output: Contribution to journalArticlepeer-review

46 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)2425-2430
Number of pages6
JournalConservation Genetics
Volume11
Issue number6
DOIs
StatePublished - Dec 2010

Keywords

  • Bottleneck
  • Connectivity
  • Conservation
  • Effective population size
  • Fragmentation
  • Linkage disequilibrium
  • Monitoring
  • N

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