The selectionist explanation

Natural selection provides an explanation for why the molecular clock depends on absolute time. Under neutral evolution, the rate of evolution is exactly the mutation rate: neutralism therefore strongly predicts a relation between number of generations and evolutionary changes. But under selection, the rate of evolution can be controlled by the pace of environmental change, which could depend on absolute time.

Suppose, for instance, that two kinds of mammal, such as a mouse (generation time approximately 0.33 years) and an elephant like the ones opposite (generation time approximately 33 years) were both separately evolving in relation to changes in parasites such as bacteria with short generation times. After 0.33 years, the bacterial population will have accumulated 0.33 years worth of change, which acts as an agent of selection on the mouse population; but after 33 years, the bacteria that parasitize elephants will have accumulated 100 times as much change, which will select 100 times as strongly on the elephants. The larger elephant generation time will to some extent be compensated by the stronger selection it will experience. The resulting rates of evolution in mice and elephants might be quite similar. The argument is simplified, but it suggests that natural selection can explain why the molecular clock keeps absolute, not generational, time.