Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 4463
Title: Accounting for missing data in estimation of contemporary genetic effective population size (Ne)
Author: David Peel, Robin S. Waples, G. M. Macbeth, Chi Do, Jennifer R. Ovenden
Publication Year: 2013
Journal: Molecular Ecology Resources
Volume: 13
Issue: 2
Pages: 243-253
Keywords: effective popluation size,missing data,linkage disequilibrium,computer simulations,temporal method

Theoretical models are often applied to population genetic datasets without fully considering the effect of missing data. Researchers can deal with missing data by removing individuals that have failed to yield genotypes and/or by removing loci that have failed to yield allelic determinations, but despite their best efforts, most datasets still contain some missing data.  As a consequence, realized sample size differs among loci, and this poses a problem for unbiased methods that must explicitly account for random sampling error.  One commonly used solution for the calculation of contemporary effective population size (Ne) is to calculate an effective sample size as an unweighted mean or harmonic mean across loci.  Although this is not ideal because it fails to account for the fact that loci with different numbers of alleles have different information content.  Here we consider this problem for genetic estimators of contemporary effective population size (Ne).  To evaluate the bias and precision of several statistical approaches for dealing with missing data, we simulated populations with known Ne and various degrees of missing data. Across all scenarios, one method of correcting for missing data (fixed-inverse variance-weighted harmonic mean) consistently performed the best for both single-sample and two-sample (temporal) methods of estimating Ne and outperformed some methods currently in widespread use.  The approach adopted here may be a starting point to adjust other population genetics methods that include per-locus sample size components.

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Theme: Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
Foci: Develop methods to use physiological and biological information to predict population-level processes.
Characterize vital rates and other demographic parameters for key species, and develop and improve methods for predicting risk and viability/sustainability from population dynamics and demographic information.