Bayesian phylogenetic analysis of combined data.

By Johan A. A. Nylander, Fredrik Ronquist, John P. Huelsenbeck, J. Nieves‐Aldrey. Systematic Biology, 2004

1,821 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/acd0f6222dd99d6500269f28f2c626ccf48c0f8c

How researchers see this paper

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

In Genetics

In Molecular Biology

In Paleontology

Citations in the corpus

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. (2012, methodology): “Of these approaches, the HME (Newton and Raftery 1994) is by far the simplest method, only requiring samples from the posterior distribution and has been used extensively in the field of phylogenetics (see, e.g., Nylander et al. 2004).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, neutral): “([52,65-67]).”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, methodology): “This first concern has largely been addressed in the past decade with the development of efficient likelihood and Bayesian algorithms permitting different data partitions to evolve under different models (e.g., Nylander et al. 2004).”
A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision (2007, methodology): “We calculated Bayes factors (Nylander et al., 2004) comparing the three partition approaches (Table 6), showing that, for the DNA123 datasets, the difference between GP and CP was much greater than that between CP and CGP.”
The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology (2009, methodology): “2 (Nylander et al. 2004) was employed to assign the best-fit likelihood settings according to the hLRT (likelihood ratio test).”
Phylogenetic species delimitation of the earthworms Eisenia fetida (Savigny, 1826) and Eisenia andrei Bouché, 1972 (Oligochaeta, Lumbricidae) based on mitochondrial and nuclear DNA sequences (2005, methodology): “This approach reduces the number of unnecessary parameters that contribute little to describing the data by penalizing more complex models (Burnham and Anderson, 2002; Nylander et al., 2004).”
The phylogeny and evolution of Figitidae (Hymenoptera: Cynipoidea) (2007, methodology): “…1992; Simon et al., 1994; Campbell et al., 2000; Wiegmann et al., 2000; Babcock et al., 2001; Dowton and Austin, 2001; Rokas et al., 2002; Schulmeister et al., 2002; Schulmeister, 2003; Heraty et al., 2004; Heraty, 2004; Lin and Danforth, 2004; Nylander et al., 2004; Nylander et al., in prep.).”
Bayesian Analysis of Molecular Evolution Using MrBayes (2005, background): “These simulation results are consistent with empirical observations of decreasing clade probabilities when the same data are analyzed under increasingly complex models [55].”
Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations (2006, background): “This reduces the number of unnecessary parameters that contribute little to describing the data by penalizing more complex models (Bernham & Anderson, 2002; Nylander et al., 2004; Posada & Buckley, 2004).”
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. (2004, methodology): “Further developments will allow for the simultaneous use of different models for different partitions of the data (Nylander et al., 2004; Pupko et al., 2002; Suchard et al., 2003a; Yang, 1996b).”
PAML 4: phylogenetic analysis by maximum likelihood. (2007, methodology): “Similar models are implemented in the Bayesian framework by Suchard et al. (2003) and Nylander et al. (2004).”
The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence (2013, background): “1.2 and proposed by Lewis (2001) and Nylander et al. (2004), with priors of all state frequencies (change rates) set equal, all topologies with equal probabilities, unconstrained branch lengths and temperature set to 0.30.”
Phylogeny, identification and nomenclature of the genus Aspergillus (2014, methodology): “Prior to the analysis, the most suitable substitution model was determined using MrModeltest 2.3 (Nylander et al. 2004), utilising the Akaike Information Criterion (AIC).”