Abstract
BackgroundThe molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others.ResultsBy applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift.ConclusionsI suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.
Highlights
The molecular clock is an important genetic tool for estimating evolutionary timescales
Application of the new rho statistic to the main events in human evolution To apply the new rho statistic described in the Methods section to real human mitochondrial DNA (mtDNA) data, a rooted tree showing the relationships of the sampled sequences is necessary
To test a more recent human colonization, I constructed a third tree including 48 already published complete mtDNA sequences belonging to the Americasspecific haplogroup B2 (Figure S3)
Summary
The molecular clock is an important genetic tool for estimating evolutionary timescales. Hominin fossils and associated Middle Stone Age artifacts from Jebel Irhoud in Morocco have recently been aged to 315 ± 34 kya [2]. These older dates were genetically confirmed in a study of ancient African genomes that estimated modern human divergence to have occurred at 350 to 260 kya [3]. Another controversial milestone of the mtDNA molecular clock is the dating of the dispersal of modern
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