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ldne: a program for estimating effective population size from data on linkage disequilibrium
Article first published online: 28 JUN 2008
DOI: 10.1111/j.1755-0998.2007.02061.x
© 2007 Blackwell Publishing Ltd. No claim to original US government works
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How to Cite
WAPLES, R. S. and DO, C. (2008), ldne: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8: 753–756. doi: 10.1111/j.1755-0998.2007.02061.x
Publication History
- Issue published online: 28 JUN 2008
- Article first published online: 28 JUN 2008
- Received 4 August 2007; revision accepted 1 November 2007
- Abstract
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Keywords:
- bias;
- genetics;
- jackknife;
- Ne/N ratio;
- precision
Abstract
ldne is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (Ne) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. ldne calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.