Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 8535
Title: Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci
Author: Ryan K. Waples, Wesley A. Larson, Robin S. Waples
Publication Year: 2016
Journal: Heredity
Abstract:

Contemporary effective population size ("N" _"e" ) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to datasets containing 10-100 loci to inform conservation and study population demography.  Performance of these "N" _"e"  estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause "N" _"e"  estimates to be downwardly biased. Here we present results from coalescent and forward simulations designed to evaluate the bias of LD-based "N" _"e"  estimates (("N" _"e"  ) ^). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r2 values, simply removing large r2 values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in ("N" _"e"  ) ^ is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of ("N" _"e"  ) ^ is much lower than expected based on the assumption that each pair of loci provides completely independent information.

Theme: Recovery and rebuilding of marine and coastal species
Foci: Characterize the population biology of species, and develop and improve methods for predicting the status of populations.
Develop methods to use physiological, biological and behavioral information to predict population-level processes.
Official Citation:

Waples RK, Larson WA, and Waples RS.  2016.  Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci.  Heredity 117:233-240