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

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.

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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. CSIRO Marine and Atmospheric Research and Wealth from Oceans Flagship, GPO Box 1538, Hobart, TAS, 7001, Australia

   Phillip R. England

2. Flathead Lake Biological Station (FLBS), University of Montana, Polson, MT, 59860, USA

   Gordon Luikart

3. Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), Universidade do Porto, 4485-661, Vairão, Portugal

   Gordon Luikart

4. NOAA Fisheries, Northwest Fisheries Science Centre, 2725 Montlake Blvd. East, Seattle, WA, 98112, USA

   Robin S. Waples

1. Phillip R. England
2. Gordon Luikart
3. Robin S. Waples

Correspondence to Phillip R. England.

England, P.R., Luikart, G. & Waples, R.S. Early detection of population fragmentation using linkage disequilibrium estimation of effective population size. Conserv Genet 11, 2425–2430 (2010). https://doi.org/10.1007/s10592-010-0112-x

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• Received: 22 September 2009

• Accepted: 13 July 2010

• Published: 24 July 2010

• Issue Date: December 2010

• DOI: https://doi.org/10.1007/s10592-010-0112-x

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