期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 28, 期 2, 页码 879-887出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msq262
关键词
heterochronous sequences; ancient DNA; molecular clock; viral evolution; measurably evolving populations
资金
- National Institute of Health [R01 GM083603, R01 GM083983, R01 GM086887]
- National Science Foundation [ARC 0909456]
- National Evolutionary Synthesis Center (NESCent), NSF [EF-0423641]
- Office of Polar Programs (OPP)
- Directorate For Geosciences [0909456] Funding Source: National Science Foundation
Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.
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