Estimating effective population size from linkage disequilibrium: severe bias in small samples

By P. England, Jean-Marie Cornuet, Pierre Berthier, David A. Tallmon, Gordon Luikart. Conservation Genetics, 2006

174 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/c26dbf6fa1cdb8be909659e1866e879cbc79b4d4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

Citations in the corpus

Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution (2009, background): “First, they presented quantitative results only for the original LD method (Hill 1981) which, when the ratio S/Ne is small, has been shown to produce an estimate that is more closely related to the sample size than to the true effective size (England et al. 2006; Waples 2006).”
Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches (2010, methodology): “However, the LD method for non-overlapping generations suffered from a severe bias until recently (England et al. 2006; Waples 2006), its performance is less well evaluated, and it has not yet been extended for use in species with over- lapping generations.”
ldne: a program for estimating effective population size from data on linkage disequilibrium (2008, methodology): “The standard linkage disequilibrium method (Hill 1981) was recently shown to be biased when sample size is less than the true (unknown) effective size (England et al .”
COMPUTER PROGRAMS: onesamp: a program to estimate effective population size using approximate Bayesian computation (2008, unknown): “Although one-sample Ne estimators hold the advantage of requiring only a single sample, they have not been used much because they are often imprecise and biased (Waples 1991; England et al. 2006).”
SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data (2015, methodology): “This has boosted the use of the method, which has been applied to humans (Tenesa et al., 2007; McEvoy et al., 2011) as well as to several domesticated species (England et al., 2006; Uimari and Tapio, 2011; Corbin et al., 2012; Kijas et al., 2012).”
A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci* (2006, methodology): “England et al. (2006) suggested that situations in which N̂e is downwardly biased using the disequilibrium method might be identified by taking a series of subsamples of increasing size from the original sample.”