Predicting nuclear gene coalescence from mitochondrial data: The three-times rule

Coalescence theory predicts when genetic drift at nuclear loci will result in fixation of sequence differences to produce monophyletic gene trees. How ever, the theory is difficult to apply to particular taxa because it hinges on genetically effective population size, which is generally unknown. Neut ral theory also predicts that evolution of monophyly will be four times slo wer in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. Variation in mitochondrial DNA (mtDNA) within an d between species has been studied extensively, but can these mtDNA data be used to predict coalescence in nuclear loci? Comparison of neutral theorie s of coalescence of mitochondrial and nuclear loci suggests a simple rule o f thumb. The "three-times rule" states that, on average, most nuclear loci will be monophyletic when the branch length leading to the: mtDNA sequences of a species is three times longer than the average mtDNA sequence diversi ty observed within that species. A test using mitochondrial and nuclear intron data from seven species of wh ales and dolphins suggests general agreement with predictions of the three- times rule. We define the coalescence ratio as the mitochondrial branch len gth for a species divided by intraspecific mtDNA diversity. We show that sp ecies with high coalescence ratios show nuclear monophyly, whereas species with low ratios have polyphyletic nuclear gene trees. As expected, species with intermediate coalescence ratios show a variety of patterns. Especially at very high or low coalescence ratios, the three-times rule predicts nucl ear gene patterns that can help detect the action of selection. The three-t imes rule may be useful as an empirical benchmark for evaluating evolutiona ry processes occurring at multiple loci.