Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 4645
Title: NEESTIMATOR v2.0: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data
Author: Chi Do, Robin S. Waples, David Peel, G. M. Macbeth, Bree J. Tillett, Jennifer R. Ovenden
Publication Year: 2013
Journal: Molecular Ecology Resources
Volume: 14
Issue: 1
Pages: 209-214
Keywords: linkage disequilibrium,

NeEstimator v2.0 is a completely revised and updated implementation of software
that produces estimates of contemporary effective population size, using several different
methods and a single input file. NeEstimator v2.0 includes three single-sample estimators
(updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new
method based on molecular co-ancestry), as well as the two-sample (moment-based temporal)
method. New features include the following: 1) An improved method for accounting for
missing data; 2) Options for screening out rare alleles; 3) Confidence intervals for all
methods; 4) The ability to analyze datasets with large numbers of genetic markers (10,000 or
more); 5) Options for batch processing large numbers of different datasets, which will
facilitate cross-method comparisons using simulated data; and 6) Correction for temporal
estimates when individuals sampled are not removed from the population (Plan I sampling).
The user is given considerable control over input data and composition, and format of output
files. The freely-available software has a new JAVA interface and runs under MacOS, Linux
and Windows.

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Theme: Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
Foci: 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.
Maximize effectiveness and minimize impacts of artificial propagation in recovery, rebuilding and stock sustainability