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Resetting the "molecular clock hypothesis"

Riv Biol. 2008 Jan-Apr;101(1):93-108. 
Ancient fossil specimens of extinct species are genetically more distant to an 
outgroup than extant sister species are.Huang S.
The Burnham Institute for Medical Research,10901 North Torrey Pines Roads, La 
Jolla, CA 92037.

There exists a remarkable correlation between genetic distance as measured by 
protein or DNA dissimilarity and time of species divergence as inferred from 
fossil records. This observation has provoked the molecular clock hypothesis. 
However, data inconsistent with the hypothesis have steadily accumulated in 
recent years from studies of extant organisms. Here the published DNA and 
protein sequences from ancient fossil specimens were examined to see if they 
would support the molecular clock hypothesis. The hypothesis predicts that 
ancient specimens cannot be genetically more distant to an outgroup than extant 
sister species are. Also, two distinct ancient specimens cannot be genetically 
more distant than their extant sister species are. The findings here do not 
conform to these predictions. Neanderthals are more distant to chimpanzees and 
gorillas than modern humans are. Dinosaurs are more distant to frogs than 
extant birds are. Mastodons are more distant to opossums than other
 placental mammals are. The genetic distance between dinosaurs and mastodons is 
greater than that between extant birds and mammals. Therefore, while the 
molecular clock hypothesis is consistent with some data from extant organisms, 
it has yet to find support from ancient fossils. Far more damaging to the 
hypothesis than data from extant organisms, which merely question the constancy 
of mutation rate, the study of ancient fossil organisms here challenges for the 
first time the fundamental premise of modern evolution theory that genetic 
distances had always increased with time in the past history of life on Earth.