NDLI: A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

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Conservation Genetics : Volume 7, Issue 1, February 2006

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Conservation Genetics : Volume 2

Conservation Genetics : Volume 1

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Content Provider	Springer Nature Link
Author	Waples, Robin S.
Copyright Year	2006
Abstract	Analysis of linkage disequilibrium ( $$\hat{r}^2$$ =mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N e) 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 N e based on $$\hat{r}^2$$ for unlinked, diallelic gene loci are sharply biased downwards ( $$\hat{N}_{\rm e}/N <0.1$$ in some cases) if sample size (S) is less than true N e. The bias is shown to arise from inaccuracies in published formula for $$E(\hat{r}^2)$$ when S and/or N e are small. Empirically derived modifications to $$E(\hat{r}^2)$$ for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in $$\hat{N}_{\rm e}<5$$ % in most cases). The modified method also performs well in estimating N e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect $$\hat{N}_{\rm e}$$ , but if N has recently increased from a bottleneck $$\hat{N}_{\rm e}$$ can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N e in natural populations. However, a comprehensive assessment of performance of $$\hat{r}^2$$ with highly polymorphic markers such as microsatellites is needed.
Starting Page	167
Ending Page	184
Page Count	18
File Format	PDF
ISSN	15660621
Journal	Conservation Genetics
Volume Number	7
Issue Number	2
e-ISSN	15729737
Language	English
Publisher	Springer Netherlands
Publisher Date	2006-03-01
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	computer simulations mating systems non-ideal populations precision sample size temporal method Evolutionary Biology Plant Sciences Animal Anatomy / Morphology / Histology Human Genetics
Content Type	Text
Resource Type	Article
Subject	Genetics Ecology, Evolution, Behavior and Systematics

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