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Testing the impact of calibration on molecular divergence times using a fossil-rich group: The case of nothofagus (Fagales)

Sauquet, Herve; Ho, Simon; Gandolfo, Maria A.; Jordan, Gregory J.; Wilf, Peter; Cantrill, David J; Bayly, Michael J; Bromham, Lindell; Brown, Gillian K; Carpenter, Raymond J.; Lee, Daphne M.; Murphy, Daniel; Sniderman, J.M. Kale; Udovicic, Frank

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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...[Show more]

dc.contributor.authorSauquet, Herve
dc.contributor.authorHo, Simon
dc.contributor.authorGandolfo, Maria A.
dc.contributor.authorJordan, Gregory J.
dc.contributor.authorWilf, Peter
dc.contributor.authorCantrill, David J
dc.contributor.authorBayly, Michael J
dc.contributor.authorBromham, Lindell
dc.contributor.authorBrown, Gillian K
dc.contributor.authorCarpenter, Raymond J.
dc.contributor.authorLee, Daphne M.
dc.contributor.authorMurphy, Daniel
dc.contributor.authorSniderman, J.M. Kale
dc.contributor.authorUdovicic, Frank
dc.date.accessioned2015-12-10T23:07:40Z
dc.identifier.issn1063-5157
dc.identifier.urihttp://hdl.handle.net/1885/62971
dc.description.abstractAlthough 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.
dc.publisherTaylor & Francis Group
dc.sourceSystematic Biology
dc.subjectKeywords: plant DNA; article; beech; biodiversity; calibration; chemistry; classification; fossil; genetic variability; genetics; methodology; phylogeny; sequence alignment; time; Biodiversity; Calibration; Classification; DNA, Plant; Fagus; Fossils; Genetic Variat age constraints; calibration; confidence intervals; Fagales; fossil record; geochronology; molecular dating; Nothofagus; Relaxed molecular clock
dc.titleTesting the impact of calibration on molecular divergence times using a fossil-rich group: The case of nothofagus (Fagales)
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume61
dc.date.issued2012
local.identifier.absfor060309 - Phylogeny and Comparative Analysis
local.identifier.ariespublicationf5625xPUB756
local.type.statusPublished Version
local.contributor.affiliationSauquet, Herve, Universite Paris-Sud
local.contributor.affiliationHo, Simon, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationGandolfo, Maria A., Cornell University
local.contributor.affiliationJordan, Gregory J., University of Tasmania
local.contributor.affiliationWilf, Peter, Pennsylvania State University
local.contributor.affiliationCantrill, David J, Royal Botanic Gardens Melbourne
local.contributor.affiliationBayly, Michael J, University of Melbourne
local.contributor.affiliationBromham, Lindell, College of Medicine, Biology and Environment, ANU
local.contributor.affiliationBrown, Gillian K, Royal Botanic Gardens Melbourne
local.contributor.affiliationCarpenter, Raymond J., University of Adelaide
local.contributor.affiliationLee, Daphne M., University of Otago
local.contributor.affiliationMurphy, Daniel, Royal Botanic Gardens Melbourne
local.contributor.affiliationSniderman, J.M. Kale, Monash University
local.contributor.affiliationUdovicic, Frank, Royal Botanic Gardens Melbourne
local.description.embargo2037-12-31
local.bibliographicCitation.issue2
local.bibliographicCitation.startpage289
local.bibliographicCitation.lastpage313
local.identifier.doi10.1093/sysbio/syr116
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2016-02-24T09:35:42Z
local.identifier.scopusID2-s2.0-84863116093
local.identifier.thomsonID000300442600009
CollectionsANU Research Publications

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