Abstract
Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.
Highlights
Accurate estimates of mutation rates are crucial for a thorough investigation of the evolutionary history of virtually any species (Ho and Larson 2006; Ho et al 2008), including ours (Scally and Durbin 2012)
We found no evidence for differences in base composition between contemporary anatomically modern humans (AMHs) and ancient AMHs (aAMHs)
No triallelic SNPs were found in the ancient sequences
Summary
Accurate estimates of mutation rates are crucial for a thorough investigation of the evolutionary history of virtually any species (Ho and Larson 2006; Ho et al 2008), including ours (Scally and Durbin 2012). Because differences between the DNA of any two individuals correspond to mutations accumulated since their common ancestor, knowing the rate at which such changes arise allows estimating the time since divergence between any two stretches of DNA This approach, referred to as “the molecular clock,” has been frequently applied to date key chapters in human evolutionary history, such as the dawn of humankind millions of years ago (Sarich and Wilson 1967; Hasegawa et al 1985; Goodman 1999; Carroll 2003) or the expansion of anatomically modern humans (AMHs) from an African cradle some 100 k years ago (Stringer and Andrews 1988; Ingman et al 2000; Stringer 2002; Cavalli-Sforza and Feldman 2003; Relethford 2008; Tattersall 2009). The most reliable calibration points for converting molecular genetic divergences among branches into absolute times remain to be identified
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