John Hawks has written about a new study which has found defects in the way that the molecular clock is used. Read his post about an explanation of the phenomenon which has led to the overestimation of divergence times.
What is important is that the new calibration leads to significantly lower estimates of events in human evolutionary history, bringing the mtDNA time depth of humanity much closer to the present, and closer to the time depth of the human Y chromosome. Perhaps though, the divergence times of human Y chromosomes may also turn out to be overestimated.
Molecular Biology and Evolution 2005 22(7):1561-1568
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
Simon Y. W. Ho et al.
Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 style="font-weight: bold;">modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution. Link