R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock

By Michael J. Sanderson. Bioinform., 2003

1,910 citations recorded by the source corpus.

Subfields: Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/3a447c53443636d33681b4ff1db57ed819f921a1

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In Molecular Biology

1. J. Doyle
2. Alexandros Stamatakis
3. Thomas L. P. Couvreur
4. Simon Y. W. Ho
5. Michael J. Donoghue
6. Nate B. Hardy
7. N. Matzke
8. John J. Wiens

In Paleontology

1. John J. Wiens
2. Michael J. Donoghue
3. Alexandros Stamatakis
4. Alexandre Antonelli
5. Simon Y. W. Ho
6. N. Matzke
7. J. Doyle
8. Nate B. Hardy

Citations in the corpus

• Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, methodology): “In addition, the geological timing and ecological context of this diversification can be estimated with aculeate fossil-calibrated molecular dating methods (Thorne et al. 1998; Kishino et al. 2001; Thorne & Kishino 2002; Sanderson 2003; Rutschmann et al. 2007); this work is in progress.”
• Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective (2007, methodology): “1995), LF Langley–Fitch, NPRS nonparametric rate smoothing, PL penalized likelihood (methods implemented in r8s; Sanderson 2003), CV Cross-validation, MP maximum parsimony, ML maximum likelihood, A and B refer to nodes in Figs.”
• Phylogeny, Molecular and Fossil Dating, and Biogeographic History of Annonaceae and Myristicaceae (Magnoliales) (2004, methodology): “This appears to be an example of an artifact sometimes encountered with NPRS that is apparently caused by the combination of an internal calibration point and near zero-length branches within the tree (M. J. Sanderson, personal communication).”
• Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae) (2010, methodology): “Whereas NPRS has been largely abandoned in favour of its successor PL [see discussion in [18]], both implemented in the software r8s [19], PL competes today in popularity with Bayesian dating [20] implemented in the software BEAST [21].”
• Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, methodology): “…constraint is especially acute for the nonparametric rate-smoothing and penalized-likelihood methods, in which there is no other information about divergence times (Sanderson 2003); it is necessary to include at least one other type of calibration, either a maximum bound or point calibration.”
• Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal Its and Chloroplast DNA Sequence Data (2008, methodology): “Because a constant rate among branch lengths was rejected, we used penalized likelihood (Sanderson 2002) with a rate smoothing parameter estimated using cross-validation using the software r8s 1.71 (Sanderson 2003).”
• Molecular phylogenetics of Myotis indicate familial-level divergence for the genus Cistugo (Chiroptera) (2010, methodology): “Using the above calibrations as point estimates, we generated a chronogram using r8s version 1.60 (Sanderson 2003) to provide a starting tree for the dating analysis.”
• Evolution and phylogeography of the tubenose goby genus Proterorhinus (Gobiidae: Teleostei): evidence for new cryptic species (2009, methodology): “To estimate divergence times, we calculated pairwise sequence divergence (using the TrN model above) within and among major Proterorhinus lineages in MEGA, version 4 (Tamura et al., 2007), and using a penalized likelihood approach in R8S, version 1.71 (Sanderson, 2003).”
• Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians (2005, methodology): “Both of these methods were performed using the computer software r8s (Sanderson, 2003).”
• Phylogenetic Relatedness Limits Co‐occurrence at Fine Spatial Scales: Evidence from the Schoenoid Sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa (2006, methodology): “.001 both trees were transformed into ultrametric trees using nonparametric rate smoothing (NPRS; Sanderson 1997) as implemented in r8s (Sanderson 2003), with rate differences weighted across the root.”
• Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa (2006, methodology): “We used the program r8s to estimate mutation rates from our data ( Sanderson 2003 ), applying the semi-parametric penalized likelihood method.”