GONe

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UPDATE! New update enables Ne estimation from cohort samples spaced any number of generations apart! See Jorde (2012) for the paper deriving the equation.
  

GONe is a user-friendly, Windows-based program for estimating effective size (Ne) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age-structure in populations. This method requires estimates of age-specific survival and birth rate, and allele frequencies measured in two or more cohorts spaced any number of generations apart. Allele frequencies are acquired by reading in genotypic data from files formatted for either Genepop or TempoFS. For each interval between cohorts, Ne is estimated at each locus and over all loci. Furthermore, Ne estimates are output for three different genetic drift estimators (Fs, Fc, and Fk). Confidence intervals are derived from a chi-square distribution with degrees-of-freedom equal to the number of independent alleles. GONe has been validated over a wide range of Ne values, and for scenarios where survival and birth rates differ between sexes, sex-ratios are unequal, and reproductive variances differ.

A paper describing GONe can be found in Molecular Ecology Resources.

Software last updated: May 10th, 2012