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Phylogenetic estimation of timescales using ancient DNA: the effects of temporal sampling scheme and uncertainty in sample ages
- Source :
- Molecular biology and evolution. 30(2)
- Publication Year :
- 2012
-
Abstract
- In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes variation in the DNA sequences and the structure of the sample ages. Various sources of estimation error can reduce our ability to estimate rates and timescales accurately and precisely. We investigated the impact of sample-dating uncertainties on the estimation of evolutionary timescale parameters using the software BEAST. Our analyses involved 11 published data sets and focused on estimates of substitution rate and root age. We show that, provided that samples have been accurately dated and have a broad temporal span, it might be unnecessary to account for sample-dating uncertainty in Bayesian phylogenetic analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise phylogenetic estimates of timescales can be made even with only a few ancient sequences. These findings have important practical consequences for studies of molecular rates, timescales, and population dynamics.
- Subjects :
- 0106 biological sciences
Population
Bayesian probability
Biology
010603 evolutionary biology
01 natural sciences
DNA, Mitochondrial
Evolution, Molecular
03 medical and health sciences
Bayes' theorem
Paleontology
Phylogenetics
Statistics
Genetics
Animals
education
Molecular clock
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Phylogeny
030304 developmental biology
0303 health sciences
education.field_of_study
Phylogenetic tree
Models, Genetic
Bayes Theorem
Ancient DNA
Sample size determination
Ursidae
Subjects
Details
- ISSN :
- 15371719
- Volume :
- 30
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- Molecular biology and evolution
- Accession number :
- edsair.doi.dedup.....c153491bad5f5888696b00f58e954edd