Time dependency of molecular rates in ancient DNA data sets, a sampling artifact? Syst Biol 58

It is common knowledge that the instantaneous rate of mutation (RoM) in DNA sequences exceeds the long-term rate of substitution (RoS) when measured in in-terspecific phylogenetic analyses. The neutral theory of molecular evolution describes this temporary excess diversity as transient polymorphisms either removed from the population through the actions of purifying selection or fixed by random genetic drift over a few generations (Kimura 1983). Observations of these “ac-celerations ” in the molecular rates within recent evolu-tionary time have been documented (Parsons et al. 1997; Lambert et al. 2002); however, they did not resolve the magnitude and duration of this phenomenon. Howell et al. (2003) have addressed these issues through pedi-gree analyses of human mitochondrial (mt) hypervari-able region (HVR) sequences and have suggested a 5- to 10-fold acceleration compared with the long-term RoS. In addition, Burridge et al. (2008) have shown that the calibration of the mt clock for galaxiid fishes using geological divergence dates with cytochrome b and control region sequences supports a transition period during which the RoM would decrease toward the RoS extending up to ∼200 kyr (Burridge et al. 2008). How-ever, the general applicability of these specific results re-mains untested. The recent publication (Ho, Phillips, Cooper, et al. 2005) of a Bayesian analysis supporting that a drastic acceleration in the molecular rates as time approaches 0 is a general and predictable feature has become a hotly debated topic in both systematics and evolutionary bi