speed‐ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples |
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| Authors: | Matthew B. Hamilton Maria Tartakovsky Amy Battocletti |
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| Affiliation: | 1. Department of Biology, Regents Hall, Georgetown University, Washington, DC, USA;2. University of Florida, Gainesville, FL, USA |
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| Abstract: | 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‐ne is a suite of matlab computer code functions to estimate  from  with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of  estimators under various population genetic scenarios. speed‐ne was 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 employed  estimator exhibited the largest variances among replicate data sets. speed‐ne implements 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‐ne provides an open‐source extensible tool for estimation of  from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare  estimators. |
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| Keywords: | confidence interval effective population size jackknife linkage disequilibrium null alleles simulation |
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) between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate 
from 
with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of 
estimators under various population genetic scenarios. speed‐ne was 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 employed 
estimator exhibited the largest variances among replicate data sets. speed‐ne implements 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‐ne provides an open‐source extensible tool for estimation of 
from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare 
estimators.