Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times

By Frank Rutschmann. 2006

218 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e2f962ce115934a83ee33720b58916a6ac82981f

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In Ecology, Evolution, Behavior and Systematics

In Genetics

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Citations in the corpus

As Time Goes by: A Simple Fool's Guide to Molecular Clock Approaches in Invertebrates* (2009, methodology): “…early studies, genetic distance matrices were used to estimate substitution rates for molecular clock estimations (e.g., Nei 1987, Li and Graur 1991), today these substitution rates are typically derived from phylogenies or from sequence data in conjunction with tree topologies (Rutschmann 2006).”
Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae) (2010, background): “The methodological and conceptual differences between r8s, BEAST, and some other methods available today for molecular dating have been reviewed by several authors [12,14,22-24].”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “In brief, methods for estimating divergence time are evolving and improving at an accelerated rate (Drummond et al., 2006; Rutschmann, 2006; Cutter, 2008).”
Monocot fossils suitable for molecular dating analyses (2015, background): “Although there are multiple sources of error in molecular dating (e.g. Magallón, 2004; Rutschmann, 2006; Lepage et al., 2007; Gandolfo, Nixon & Crepet, 2008; Parham & Irmis, 2008; Ho & Phillips, 2009; Clarke, Warnock & Donoghue, 2011; Parham et al., 2012; Dos Reis & Yang, 2013; Paradis, 2013; Sauque”
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, methodology): “The available relaxed-clock methods have been compared in several reviews (Magallón 2004; Welch and Bromham 2005; Lepage et al. 2006; Rutschmann 2006), and their performance has been assessed in a number of studies (e.g., Ho et al. 2005; Drummond et al. 2006; Lepage et al. 2007).”
Molecular dating of the ‘Gondwanan’ plant family Proteaceae is only partially congruent with the timing of the break‐up of Gondwana (2007, background): “Molecular dating methods have now improved to a point at which problems such as rate heterogeneity can be accommodated to some extent (Magallón, 2004; Rutschmann, 2006), but in order for such fossil-calibrated studies to provide realistic dates, the fossils chosen to act as calibration or constraint”
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini) (2010, unknown): “assigning a strict sequence divergence rate might not capture variation in mtDNA rates across a tree (Rutchmann, 2006).”
Area and the rapid radiation of Hawaiian Bidens (Asteraceae) (2012, unknown): “considered reliable for age estimation (Rutschmann, 2006).”
Estimating the timing of early eukaryotic diversification with multigene molecular clocks (2011, unknown): “Relaxed clock approaches account for heterogeneity in evolutionary rates across branches and enable the use of complex models of sequence evolution (reviewed in 16, 17), although debate continues as to the best method for relaxing the clock (18-20).”
A revised evolutionary history of Poales: origins and diversification (2014, background): “It can also estimate parameters of the prior distributions instead of having to specify these in other molecular dating methods (Rutschmann, 2006).”