Clock debate: when times are a-changin': Time dependency of molecular rate estimates: tempest in a teacup

Did dung beetles arise in Africa? A phylogenetic hypothesis based on five gene regions

“…The use of molecular clocks has been extensively debated; for details see Bromham and Penny (2003), Hedges and Kumar (2003), Graur and Martin (2004), Bandelt (2008), Ho and Larson (2006) and Howell and Howell (2008). We acknowledge the uncertainties surrounding calibration points and estimated times of divergence should be interpreted with much caution.…”

Mitochondrial phylogeography of the European ground squirrel, Spermophilus citellus, yields evidence on refugia for steppic taxa in the southern Balkans

“…Their divergence rate (approximately 2% net distance per Myr) estimate was based on the molecular data developed for Spermophilus by Harrison et al, 2003. This substitution rate is probably dependent on the calibration point (see Ho et al, 2005Ho et al, , 2007, and more data are needed before any sort of time dependence of estimated rates can be formulated and evaluated over the expected divergence times (Bandelt, 2008).…”

Phylogeographic analysis of the mid-Holocene Mammoth from Qagnaxˆ Cave, St. Paul Island, Alaska

“…Calculations were also greatly affected by the inclusion or exclusion of an outgroup sequence and whether or not constraints on the coalescent times were implemented (e.g., between the Asian elephant and mammoths). This is not surprising, as there has been considerable recent debate (Woodhams, 2006;Ho et al, 2007;Bandelt, 2007) on the reliability of calculated evolutionary rates, such that temporal inferences are especially affected by the relative depth of inquiry (i.e., timing of samples-outgroup common ancestry). However, there are good reasons to believe that sequence data from a closely related species would aid in temporal inferences (Ho and Larson, 2006).…”