has passed, many sites have undergone more than one change, but it is impossible to detect more than one. This means that the observed number of changes is no longer linear with time, but instead flattens out. Even at intermediate genetic distances, with phylogenetic data still sufficient to estimate topology, signal for the overall scale of the tree can be weak under complex likelihood models, leading to highly uncertain molecular clock estimates. At very short time scales, many differences between samples do not represent fixation of different sequences in the different populations. Instead, they represent alternative alleles that were both present as part of a polymorphism in the common ancestor. The inclusion of differences that have not yet become fixed leads to a potentially dramatic inflation of the apparent rate of the molecular clock at very short timescales. Uses The molecular clock technique is an important tool in molecular systematics, macroevolution, and phylogenetic comparative methods. Estimation of the dates of phylogenetic events, including those not documented by fossils, such as the divergences between living taxa has allowed the study of macroevolutionary processes in organisms that had limited fossil records. Phylogenetic comparative methods rely heavily on calibrated phylogenies. In applications over deep time scales, the limitations of the molecular clock hypothesis (above) must be considered; such estimates may be off by 50% or more. See also Charles Darwin Gene orders Human mitochondrial molecular clock Mitochondrial Eve and Y-chromosomal Adam Models of DNA evolution Molecular evolution Neutral theory of molecular evolution References Further reading External links Allan Wilson and the molecular clock Molecular clock explanation of the molecular equidistance phenomenon Date-a-Clade service for the molecular tree of life Evolutionary biology concepts Molecular evolution Molecular genetics Phylogenetics