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Title: speed‐ne : Software to simulate and estimate genetic effective population size ( N e ) from linkage disequilibrium observed in single samples

The genetic effective population size,Ne, can be estimated from the average gametic disequilibrium () between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals.speed‐neis a suite ofmatlabcomputer code functions to estimatefromwith a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators.speed‐neincludes functions to either generate or input simulated genotype data to facilitate comparative studies ofestimators under various population genetic scenarios.speed‐newas validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on,how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact. Estimators differed greatly in precision in the scenarios examined, and a widely employedestimator exhibited the largest variances among replicate data sets.speed‐neimplements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies.speed‐neprovides an open‐source extensible tool for estimation offrom empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compareestimators.

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Author(s) / Creator(s):
 ;  ;  
Publisher / Repository:
Date Published:
Journal Name:
Molecular Ecology Resources
Page Range / eLocation ID:
p. 714-728
Medium: X
Sponsoring Org:
National Science Foundation
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