U.S. Department of Commerce


Date of this Version



Genetics 175: 219–233 ( January 2007); DOI: 10.1534/genetics.106.065300


The standard temporal method for estimating effective population size (Ne) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates ˆNe caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased ˆNe. The direction and magnitude of the bias are shown to depend on the sampling method and the species’ life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde–Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.