Phylogeny estimation: traditional and Bayesian approaches

By Mark T. Holder, Paul O. Lewis. Nature reviews genetics, 2003

643 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/991f3736c376d5395d94408572a8f46949ab649b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Andrew Rambaut
2. I. Sanmartín
3. Hervé Philippe
4. Alexei J. Drummond
5. John P. Huelsenbeck
6. Fredrik Ronquist
7. Nicolas Lartillot
8. David Posada

In Molecular Biology

1. Alexandros Stamatakis
2. Hervé Philippe
3. Andrew Rambaut
4. Nicolas Lartillot
5. T. Buckley
6. John P. Huelsenbeck
7. Alexei J. Drummond
8. I. Sanmartín

In Paleontology

1. I. Sanmartín
2. Alexandros Stamatakis
3. Andrew Rambaut
4. Johan A. A. Nylander
5. John P. Huelsenbeck
6. Fredrik Ronquist
7. David Posada
8. T. Buckley

Citations in the corpus

• Restoring species through reintroductions: strategies for source population selection (2015, methodology): “Similarity is typically estimated from phylogenetic relationships or historical gene flow calculated using genetic markers (for methods see Holder & Lewis 2003; San Mauro & Agorreta 2010; Marko & Hart 2011).”
• TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses (2010, positive): “The recent invasion of phylogenetics by Bayesian techniques (e.g., [1]), the ever improving models and algorithms for tree searches under maximum likelihood (e.g., [2,3]), and the continuously growing processor speed helped these previously computationally very expensive approaches to become a…”
• RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees (2005, methodology): “A useful review of traditional and bayesian approaches is available from Holder and Lewis (2003).”
• Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. (2008, methodology): “Such methods have become increasingly popular and practical over recent years (Holder and Lewis, 2003).”
• The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea) (2007, methodology): “Bayesian inference of phylogeny using MCMC (reviewed in Holder and Lewis, 2003) provides a powerful alternative to parsimony for phylogenetic and evolutionary analysis.”
• BAYESIAN BETA REGRESSION: APPLICATIONS TO HOUSEHOLD EXPENDITURE DATA AND GENETIC DISTANCE BETWEEN FOOT‐AND‐MOUTH DISEASE VIRUSES (2007, methodology): “Most methods for comparing genetic distances of isolates utilize phylogenetic tree models, using neighbor-joining, parsimony, maximum likelihood, bootstrap or Bayesian methods of analysis (Holder & Lewis, 2003).”
• Computing Bayes factors using thermodynamic integration. (2006, methodology): “In addition, general numerical methods based on Markov Chains Monte Carlo (MCMC) have been developed, allowing one to conduct Bayesian inferences under a large category of probabilistic models, with few constraints on dimensionality or analytical integrability (Gelman et al., 2004; Holder and Lewis,”
• Phylogenomics and the reconstruction of the tree of life (2005, methodology): “The three main types of standard phylogenetic reconstruction method (distance,parsimony and likelihood methods 10 ; BOX 1 ) have been adapted for use in life 5 .”
• The phylogeny of Arthoniales (Pezizomycotina) inferred from nucLSU and RPB2 sequences (2011, methodology): “Bayesian inference (Holder and Lewis 2003; Huelsenbeck et al. 2001) and parsimony analyses were used to estimate the phylogenetic relationships.”
• Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, methodology): “…accommodate these properties have a much larger influence on the outcome of a molecular phylogenetic analysis than the particular method chosen to build a tree [although there are good reasons for preferring some phylogenetic methods over others (Holder & Lewis 2003; Swofford et al. 1996, 2001)].”
• Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes) (2006, background): “Bayesian inference (see e.g. Holder & Lewis 2003; Huelsenbeck et al .”
• Inferring dispersal: a Bayesian approach to phylogeny‐based island biogeography, with special reference to the Canary Islands (2008, background): “Changes that improve the likelihood of the model are always accepted; otherwise, they are accepted with a probability proportional to the ratio of the likelihood of the new state compared with that of the previous state in the chain (Holder & Lewis, 2003; Nylander et al., 2004; Pagel et al., 2004).”
• Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. (2004, background): “Indeed, posterior probabilities of trees are already being used to estimate phylogenies (Holder and Lewis, 2003; Huelsenbeck et al., 2001, 2002; Larget and Simon, 1999; Mau and Newton, 1997; Mau et al., 1999; Yang and Rannala, 1997).”