Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.

By Ziheng Yang, Bruce Rannala. Molecular biology and evolution, 2006

821 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/99feed2a098510899e050cf88985a26491c5f11c

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Citations in the corpus

Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “It is desirable to have as many calibration points as possible and new methods that improve the ability to incorporate uncertainty into fossil dates are an important step forward (Yang & Rannala 2006).”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, methodology): “The program now implements the MCMC algorithm for dating species divergences of Yang and Rannala (2006) and Rannala and Yang (2007).”
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera (2012, background): “Some of these artifacts can be avoided by using soft instead of hard bounds on the calibration ages (Yang and Rannala 2006).”
Calibrating molecular estimates of substitution rates and divergence times in birds (2007, background): “While this technique is strictly valid, the distillation of fossil data into simple minimum bounds is not ideal because it discards potentially useful information ( Yang and Rannala 2006 ).”
A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. (2015, background): “The crucial relevance of independent calibrations in relaxed clock analyses has been recognized (e.g. Aris-Brosou & Yang, 2003; Smith et al., 2006; Yang & Rannala, 2006; Donoghue & Benton, 2007; Ho, 2007; Rannala & Yang, 2007; Wilkinson et al., 2011), and also that relaxed clock models may…”
Taxon sampling and the accuracy of phylogenetic analyses (2008, methodology): “…the sensitivity of divergence time estimation methods to fossil calibration choice (Near & Sanderson, 2004; Near et al., 2005; Roger & Hug, 2006; Yang & Rannala, 2006; Ho, 2007; Hugall et al., 2007; Rutschmann et al., 2007), together with studies emphasizing the importance of increased taxon…”
A phylogeny and timescale for the living genera of kangaroos and kin (Macropodiformes : Marsupialia) based on nuclear DNA sequences (2008, background): “GTR+G+ I), does not assume autocorrelation of rates among lineages and permits both “soft” and “hard” node constraints (Hedges and Kumar 2004; Yang and Rannala 2006).”
Higher‐level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences (2019, methodology): “For the molecular clock analysis, a birth-death prior on divergence time and fossil calibrations with soft bounds (Yang & Rannala, 2006) were used.”
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, methodology): “…have soft fossil calibrations: t10 ~ B (0.5, 1.5), t12 ~ B(0.1, 0.3), t13 ~ B (0.3, 0.5) and t16 ~ B (0.2, 0.4), where, for example, B (0.5, 1.5) means that the divergence time is between 5 and 15 Ma in the young phylogeny, or between 50 and 150 Ma in the old phylogeny (Yang and Rannala, 2006).”
A Divergence Dating Analysis of Turtles Using Fossil Calibrations: An Example of Best Practices (2013, background): “Since that study, advances in Bayesian statistical phylogenetics (Drummond et al., 2006; Yang, 2006; Yang and Rannala, 2006) allow calibrations to encompass a range of dates.”
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary (2008, neutral): “Rannala [ 22 ]. We found significant correlations for both the unpartitioned and partitioned”
Class of multiple sequence alignment algorithm affects genomic analysis. (2013, background): “The choice of MSAM class may also affect other downstream analyses where branch lengths play an important role, such as molecular dating methods (Drummond et al. 2006; Yang and Rannala 2006) or understanding speciation and diversiﬁcation of species (Stadler 2011).”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “Bayesian (Thorne et al., 1998; Kishino et al., 2001; Thorne and Kishino, 2002; Yang and Rannala, 2006) and likelihood (Yang and Yoder, 2003; Yang, 2004) methods have been developed and modified such that they can account for violations of the molecular clock and for uncertainties of the fossil…”
The timescale of early land plant evolution (2018, neutral): “As the volume of sequence data increases, it is anticipated that clade age estimates should converge on a straight line, with residual dispersion reflecting uncertainty in calibrations that cannot be overcome by additional sequence data (38).”
Best Practices for Justifying Fossil Calibrations (2011, background): “Most studies use a Bayesian framework for estimating divergence dates with probability curves between a minimum and a maximum bound to represent calibrations (time priors) (Thorne et al. 1998; Drummond et al. 2006; Yang 2006; Yang and Rannala 2006).”
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, methodology): “To address these shortcomings, Yang and Rannala (2006) proposed soft bounds, which assign a nonzero probability to all age values (Fig.”