Calibrating molecular estimates of substitution rates and divergence times in birds

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A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. (2015, background): “…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 insufficiently capture the degree of molecular…”
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, methodology): “The new relaxed-clock methods have also introduced more flexible techniques for incorporating calibrations, leading to a lively discussion about approaches to calibrating estimates of divergence times (Graur and Martin 2004; Hedges and Kumar 2004; Donoghue and Benton 2007; Ho 2007).”
As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, background): “…from the fact that they can provide only minimum age estimates as a fossil is necessarily younger than the phylogenetic event that led to its existence and as there is an inherent problem with missing taxa (Marshall 1990, Cutler 2000, Hedges and Kumar 2004, Benton and Donoghue 2007, Ho 2007).”