NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data |
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Authors: | C Do R S Waples D Peel G M Macbeth B J Tillett J R Ovenden |
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Institution: | 1. Conservation Biology Division, Northwest Fisheries Science Center, , 2725 Montlake Blvd East, Seattle, WA 98112, USA;2. Northwest Fisheries Science Centre, NOAA Fisheries, , 2725 Montlake Blvd East, Seattle, WA 98112, USA;3. CSIRO Computational Informatics, , Hobart, Tas., 7004 Australia;4. Queensland Department of Agriculture, Fisheries and Forestry, 80 Ann St., , Brisbane, Qld 4000, Australia;5. Australian Institute of Marine Science, UWA Oceans Institute, , Crawley, WA, 6009 Australia;6. Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, , Otto Hirschfeld Building (81), St Lucia, Qld, 4072 Australia |
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Abstract: | NeEstimator v2 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 includes three single‐sample estimators (updated versions of the linkage disequilibrium and heterozygote‐excess methods, and a new method based on molecular coancestry), as well as the two‐sample (moment‐based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross‐method comparisons using simulated data; and (vi) 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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Keywords: | heterozygote‐excess linkage disequilibrium molecular coancestry Plan I and II temporal sampling |
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