Estimating genetic drift and effective population size from temporal shifts in dominant gene marker frequencies

Measurement of temporal change in allele frequencies represents an indirect method for estimating the genetically effective size of populations. When allele frequencies are estimated for gene markers that display dominant gen e expression, such as, e.g. random amplified polymorphic DNA (RAPD) and amp lified fragment length polymorphism (AFLP) markers, the estimates can be se riously biased. We quantify bias for previous allele frequency estimators a nd present a new expression that is generally less biased and provides a mo re precise assessment of temporal allele frequency change. We further devel op an estimator for effective population size that is appropriate when deal ing with dominant gene markers. Comparison with estimates based on codomina ntly expressed genes, such as allozymes or microsatellites, indicates that about twice as many loci or sampled individuals are required when using dom inant markers to achieve the same precision.