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      Linkage disequilibrium estimates of contemporary N e using highly variable genetic markers: a largely untapped resource for applied conservation and evolution

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          Abstract

          Genetic methods are routinely used to estimate contemporary effective population size ( N e) in natural populations, but the vast majority of applications have used only the temporal (two-sample) method. We use simulated data to evaluate how highly polymorphic molecular markers affect precision and bias in the single-sample method based on linkage disequilibrium (LD). Results of this study are as follows: (1) Low-frequency alleles upwardly bias , but a simple rule can reduce bias to <about 10% without sacrificing much precision. (2) With datasets routinely available today (10–20 loci with 10 alleles; 50 individuals), precise estimates can be obtained for relatively small populations ( N e < 200), and small populations are not likely to be mistaken for large ones. However, it is very difficult to obtain reliable estimates for large populations. (3) With ‘microsatellite’ data, the LD method has greater precision than the temporal method, unless the latter is based on samples taken many generations apart. Our results indicate the LD method has widespread applicability to conservation (which typically focuses on small populations) and the study of evolutionary processes in local populations. Considerable opportunity exists to extract more information about N e in nature by wider use of single-sample estimators and by combining estimates from different methods.

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          Most cited references51

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          Estimation of average heterozygosity and genetic distance from a small number of individuals.

          M Nei (1978)
          The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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            A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

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              Estimation of effective population size from data on linkage disequilibrium

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                Author and article information

                Journal
                Evol Appl
                Evol Appl
                eva
                Evolutionary Applications
                Blackwell Publishing Ltd (Oxford, UK )
                1752-4571
                1752-4571
                May 2010
                24 November 2009
                : 3
                : 3
                : 244-262
                Affiliations
                [1 ]simpleNOAA Fisheries, Northwest Fisheries Science Center Seattle, WA, USA
                [2 ]simpleConservation Biology Division, Northwest Fisheries Science Center Seattle, WA, USA
                Author notes
                Robin S. Waples, NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd. East, Seattle, WA 98112, USA. Tel.: (206) 860 3254; fax: (206) 860 3335; e-mail: robin.waples@ 123456noaa.gov
                Article
                10.1111/j.1752-4571.2009.00104.x
                3352464
                25567922
                2a7c71c8-f605-4ca4-aea5-46398ca93c31
                © 2009 Blackwell Publishing Ltd
                History
                : 14 August 2009
                : 11 October 2009
                Categories
                Original Articles

                Evolutionary Biology
                bias,effective population size,computer simulations,confidence intervals,precision,microsatellites,temporal method

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