Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

By Simon Y. W. Ho, M. J. Phillips, Alan Cooper, Alexei J. Drummond. Molecular biology and evolution, 2005

1,052 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/52af4b3cb7722bc7931341f25c5702381e15c6bb

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Citations in the corpus

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone (2011, background): “Because of potential problems associated with model parameter variance across heterogeneous datasets (Ho, 2005; Guiher & Burbrink, 2008), divergence estimates were inferred for a reduced dataset,”
The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, background): “However, while RHAS has been put forward as a potential explanation for the time dependence of rates (Ho et al. 2005, 2007; Galtier et al. 2006; Henn et al. 2009), this has not been validated theoretically and the effects on molecular estimates of divergence times remain poorly explored.”
Mitochondrial DNA as a marker of molecular diversity: a reappraisal (2009, background): “A proper description of the mitochondrial mutation process could help resolving the paradox raised by Ho et al. (2005), who consistently reported a faster mtDNA molecular clock at recent vs. ancient time scale.”
Warring brothers: The complex interactions between wolves (Canis lupus) and dogs (Canis familiaris) in a conservation context (2014, neutral): “, 1997), but the use of molecular clocks has been critiqued for recent divergences (Ho et al., 2005).”
Molecular phylogeny and evolution of the Asian lineage of vole genus Microtus (Rodentia: Arvicolinae) inferred from mitochondrial cytochrome b sequence (2010, background): “In our molecular clock analysis, we attempt to accommodate the phenomenon of rate decay (time dependency of rate estimates) that might have serious implications for dating recent (< 1–2 Mya) evolutionary events (Ho et al., 2005, 2008; Henn et al., 2009).”
Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. (2010, background): “Following Ho et al. (2005), the constant k represents the ‘‘long-term’’ substitution rate, which was k 5 1.”
Calibrating the avian molecular clock (2008, background): “Recently, several authors have suggested that molecular rates are time dependent with the fastest rates obtained from calibration points near the recent (Garcia-Moreno 2004; Ho et al. 2005; Penny 2005).”
Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north‐western Eurasia (2013, methodology): “To minimize the impact of purifying selection, which can influence age estimates of recent evolutionary events (Ho et al., 2005), we limited this analysis to the third codon sites of the mitochondrial protein-coding genes.”
Genetics and animal domestication: new windows on an elusive process (2006, background): “Lastly, a recent paper (Ho et al., 2005) argues that rates of sequence evolution are heavily dependent on the time depth of relationships within the dataset used to derive the rate.”
A Taxonomic Reassessment of Cacajao melanocephalus Humboldt (1811), with the Description of Two New Species (2008, background): “1979) and the upper-bound (1.5% per million yr; Ho et al. 2005) substitution rates result in an estimate of the last common ancestor of Neblina and Aracá uakaris at 0.”