TY - JOUR
T1 - Testing the impact of calibration on molecular divergence times using a fossil-rich group
T2 - The case of nothofagus (Fagales)
AU - Sauquet, Hervé
AU - Ho, Simon Y.W.
AU - Gandolfo, Maria A.
AU - Jordan, Gregory J.
AU - Wilf, Peter
AU - Cantrill, David J.
AU - Bayly, Michael J.
AU - Bromham, Lindell
AU - Brown, Gillian K.
AU - Carpenter, Raymond J.
AU - Lee, Daphne M.
AU - Murphy, Daniel J.
AU - Sniderman, J. M.Kale
AU - Udovicic, Frank
N1 - Funding Information:
FUNDING This work was initiated through a workshop funded by the Australian Research Council–New Zealand Research Network for Vegetation Function (Working Group 32, “Calibrating the Evolutionary History of Southern Hemisphere Plant Clades”), held in 2008 at the Royal Botanic Gardens, Melbourne, and organized by M.A.G., D.J.C., and P.W. We thank Mark Westoby for his dynamic leadership of the Network and encouragement of this Working Group. Additional support came from NSF [DEB-0919071 to P.W. and M.A.G., DEB-0345750 to P.W. and M.A.G., DEB-0918932 to M.A.G.].
PY - 2012/3
Y1 - 2012/3
N2 - Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro-and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.
AB - Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro-and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.
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U2 - 10.1093/sysbio/syr116
DO - 10.1093/sysbio/syr116
M3 - Article
C2 - 22201158
AN - SCOPUS:84863116093
VL - 61
SP - 289
EP - 313
JO - Systematic Biology
JF - Systematic Biology
SN - 1063-5157
IS - 2
ER -