Improved calibration of the human mitochondrial clock using ancient genomes - PubMed (original) (raw)

Improved calibration of the human mitochondrial clock using ancient genomes

Adrien Rieux et al. Mol Biol Evol. 2014 Oct.

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.

Keywords: Bayesian phylogenetic inference; ancient genomes; calibration strategy; divergence times; human; mitochondrial substitution rates; molecular clock.

© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

PubMed Disclaimer

Figures

F<sc>ig</sc>. 1.

Fig. 1.

Phylogenetic tree built on a subset of both contemporary and ancient samples. This phylogeny was constructed with the BEAST software using 59 cAMHs, 21 aAMHs, and 5 archaic Neanderthals. The topology presented is well resolved as all nodes exhibit a posterior probability greater than 0.9. The end depth of branches for ancient samples reflects their ages. Ancient and contemporary samples are indicated with rectangles and circles, respectively, and colors indicate their geographical origin. Date estimates for major divergence events estimated using tips calibration are shown at the nodes. The number next to the red stars indicates the colonization/migration event associated with the node.

F<sc>ig</sc>. 2.

Fig. 2.

Estimates of the TMRCA of all AMHs. Box plot (minimum, quartiles, median, and maximum) for Bayesian estimates of the TMRCA of all modern humans (in Ma) obtained under various calibration scenarios.

F<sc>ig</sc>. 3.

Fig. 3.

Variation in substitution rate among individual calibrations. Substitution rate estimates obtained using individual tip and node calibrations are reported for the whole mtDNA (in µ/site/year). Results are reported as 95% HPD intervals. Individual tips and nodes are sorted by their respective ages (given in years in brackets, see

supplementary appendices S3

and

S4

,

Supplementary Material

online, for details). Global estimates obtained using all tips or all internal nodes simultaneously for calibration, as well as root-based estimate are also given for comparison.

F<sc>ig</sc>. 4.

Fig. 4.

TMRCAs of AMHs obtained under different phylogenetic parameters. TMRCAs (in Ma) between all pairs of samples (belonging to the AMH clade only) obtained under different phylogenetic reconstruction parameters. The topology of the tree obtained using the full data (all sites in the mtDNA, see

supplementary appendix S9

,

Supplementary Material

online) has been fixed in BEAST. Panel (A) represents TMRCAs estimated the PC3 versus PC1+2 subsets of nucleotides. The solid line shows y = x line, and the dashed line is a polynomial regression of degree 2. Panel (B) represents the age of all nodes when independently estimated using either a strict or relaxed clock; the linear regression coefficient between the two sets of nodes is _R_2 = 0.98.

Similar articles

Cited by

References

    1. Atkinson QD, Gray RD, Drummond AJ. MtDNA variation predicts population size in humans and reveals a major southern Asian chapter in human prehistory. Mol Biol Evol. 2008;25:468–474. - PubMed
    1. Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol. 2012;29:2157–2167. - PMC - PubMed
    1. Baele G, Li WLS, Drummond AJ, Suchard MA, Lemey P. Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol Biol Evol. 2013;30:239–243. - PMC - PubMed
    1. Balloux F. The worm in the fruit of the mitochondrial DNA tree. Heredity. 2010;104:419–420. - PubMed
    1. Balloux F, Handley L-JL, Jombart T, Liu H, Manica A. Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation. Proc Biol Sci. 2009;276:3447–3455. - PMC - PubMed

Publication types

MeSH terms

Grants and funding

LinkOut - more resources