U.S. Department of Commerce


Date of this Version



Conservation Genetics (2006) 7:167–184; DOI 10.1007/s10592-005-9100-y


Analysis of linkage disequilibrium (ȓ2=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (Ne) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of Ne based on ȓ2 for unlinked, diallelic gene loci are sharply biased downwards ( N^e=N<0.1 in some cases) if sample size (S) is less than true Ne. The bias is shown to arise from inaccuracies in published formula for E (ȓ2) when S and/or Ne are small. Empirically derived modifications to E(ȓ2) for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in N^e < 5% in most cases). The modified method also performs well in estimating Ne in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect N^e, but if N has recently increased from a bottleneck N^e can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary Ne in natural populations. However, a comprehensive assessment of performance of ȓ2with highly polymorphic markers such as microsatellites is needed.