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Originally published as Genetics Published Articles Ahead of Print on November 16, 2006.
Genetics, Vol. 175, 219-233, January 2007, Copyright © 2007
doi:10.1534/genetics.106.065300
Temporal Estimates of Effective Population Size in Species With Overlapping Generations
Robin S. Waples*,1 and
Masashi Yokota*,
* Northwest Fisheries Science Center, Seattle, Washington 98112 and Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
1 Corresponding author: Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112.
E-mail: robin.waples{at}noaa.gov
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 
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 . 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.
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