Time-Dependency of Molecular Rates in Ancient DNA Datasets, a Sampling Artifact?
Here we examine how a variety of factors (including calibration methods, sequence length, etc) affect divergence estimates in BEAST.
Jul 01, 2009
Authors: R. Debruyne, H. N. Poinar
Systematic Biology, Vol. 58, Issue 3, pp. 348–360, June 2009. DOI: https://doi.org/10.1093/sysbio/syp028
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 interspecific 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 "accelerations" in the molecular rates within recent evolutionary 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 pedigree analyses of human mitochondrial (mt) hypervariable 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). However, the general applicability of these specific results remains untested...