Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times.

By Simon Y. W. Ho, M. J. Phillips. Systematic Biology, 2009

862 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/992b3a94658c58e33a9f9c6d39b4847ad14e8e64

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Paleontology

Citations in the corpus

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification (2019, background): “The joint use of fossils at both deep and shallow nodes may produce interaction among the calibrations because the node ages in a tree are not mutually independent (Ho & Phillips, 2009).”
Vicariance or long‐distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae) (2011, methodology): “We also accounted for uncertainty in the placement of calibration points to either stem or crown nodes (Magallón, 2004; Renner, 2005; Ho & Phillips, 2009).”
Estimating the timing of early eukaryotic diversification with multigene molecular clocks (2011, background): “Fossils provide minimum dates, leaving open the possibility that clades evolved much earlier than their first fossil appearance (2, 31).”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, methodology): “Note that these are the same input data required for divergence time estimation using calibration density approaches (29, 31, 32).”
Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone (2011, background): “These lognormal distributions with hard lower bounds best reflect the prediction, based on the high likelihood of fossil non-preservation, that any true divergence date will probably be older than the oldest known fossil, rather than younger (Ho & Phillips, 2009; Kelly et al., 2009).”
Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes (2011, background): “These lognormal distributions with hard lower bounds best reflect the prediction, based on the high likelihood of fossil nonpreservation, that any true divergence date will probably be older than the oldest known fossil, rather than younger (Ho & Phillips, 2009; Kelly et al., 2009).”
FOSSIL CALIBRATIONS FOR THE ARTHROPOD TREE OF LIFE (2016, background): “…and accuracy of date estimates are improved with the inclusion of as many a priori justified fossils as possible in tip-(Lee et al., 2013; Ronquist et al., 2012; Zhang et al., or node-dating studies (Heath et al., 2014; Ho and Phillips, 2009; Warnock et al., 2012, 2015; Yang and Rannala, 2006).”
Best Practices for Justifying Fossil Calibrations (2011, background): “Researchers who use this intuitive approach should provide detailed arguments justifying their decisions so that others can evaluate them and, following the arguments of Benton and Donoghue (2007) and Ho and Phillips (2009), the maximum bounds should be soft and liberal.”
A Divergence Dating Analysis of Turtles Using Fossil Calibrations: An Example of Best Practices (2013, background): “Furthermore, it has been demonstrated that calibrations have a pejorative impact on the accurate estimation of evolutionary rates and dates (Ho and Phillips, 2009; Inoue et al., 2010; Clarke et al., 2011; Warnock et al., 2012; dos Reis et al., 2012).”
Flammable biomes dominated by eucalypts originated at the Cretaceous-Palaeogene boundary. (2011, methodology): “The phylogeny was estimated both with and without internal constraints to test whether calibration affected the topolog”
Testing geological models of evolution of the Isthmus of Panama in a phylogenetic framework (2013, neutral): “Normally distributed priors have been shown to be most appropriate for modelling secondary calibrations because they reﬂect the uncertainty in age estimates (Ho, 2007; Ho & Phillips, 2009).”
Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography (2013, background): “However, in the case of fossil evidence the exponential prior distribution is generally preferred because it assigns a minimum hard bound, implying that the node in question cannot be younger than the age of the fossil (Ho & Phillips, 2009).”
‘Out‐of‐Africa’ dispersal of tropical floras during the Miocene climatic optimum: evidence from Uvaria (Annonaceae) (2012, background): “A lognormal prior distribution is appropriate for a calibration based on fossil data as the divergence event is likely to have occurred prior to the appearance of the earliest fossil (Ho & Phillips, 2009).”
The peril of dating beetles (2017, background): “Likewise, the choice of fossil calibration prior densities should be examined in a comparative framework (Ho & Phillips, 2009).”