Incomplete taxon sampling is not a problem for phylogenetic inference

By M. Rosenberg, Sudhir Kumar. Proceedings of the National Academy of Sciences of the United States of America, 2001

325 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/2936d58be7363d96a98a93429a7894ee05ea9e7d

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. Sudhir Kumar
2. Koichiro Tamura
3. Glen Stecher
4. Masatoshi Nei
5. John J. Wiens
6. Derrick J. Zwickl
7. S. Blair Hedges
8. Daniel Peterson

In Molecular Biology

1. Sudhir Kumar
2. Koichiro Tamura
3. Glen Stecher
4. Masatoshi Nei
5. S. Blair Hedges
6. J. Conrad
7. Derrick J. Zwickl
8. John J. Wiens

In Paleontology

1. John J. Wiens
2. J. Conrad
3. Derrick J. Zwickl
4. Glen Stecher
5. P. B. Matheny
6. S. Blair Hedges
7. Koichiro Tamura
8. R. Vrijenhoek

Citations in the corpus

• Taxonomic aspects of Peronosporaceae inferred from Bayesian molecular phylogenetics (2003, result): “The use of more characters instead of more taxa is in accordance with the results of recent simulation studies (Rosenberg and Kumar 2001; Whelan et al. 2001).”
• Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development (2005, background): “More complete taxon sampling (Hillis 1998) and/or analysis of additional gene regions (Rosenberg & Kumar 2001) is required to enhance the resolution of the phylogenetic relationships and allow a more complete understanding of Macrobrachium evolution.”
• Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion (2006, methodology): “It has also become well accepted that probabilistic model-based methods are the superior choice for phylogenetic inference, in part because of studies demonstrating their higher accuracy (Huelsenbeck and Hillis, 1993; Huelsenbeck, 1995; Rosenberg and Kumar, 2001; Zwickl and Hillis, 2002).”
• The Xylariales: A monophyletic order containing 7 families (2003, background): “It has been shown that increasing the number of characters also increases the level of support and phylogenetic accuracy of an analysis (Huelsenbeck, 1995; Poe and Swofford, 1999; Moncalvo et al., 2000; Rosenberg and Kumar, 2001), which is clear from the results presented here as the combined analys”
• Missing data and the design of phylogenetic analyses (2006, background): “For example, there has been considerable debate in recent years over the merits of sampling more characters versus taxa for a given phylogenetic study [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23].”
• The origin and evolution of model organisms (2002, result): “However, the results of TAXON SAMPLING simulation”
• Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology (2008, background): “That increasing taxon sampling is beneficial was recently challenged by an evolutionary model using DNA evidence (Rosenberg and Kumar, 2001).”
• Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe; Agaricales). (2005, background): “Although nearly 2400 nucleotide sites were sequenced in that study, the addition of loci and an increase in taxon sample size is believed to raise overall conWdence and resolution throughout a phylogenetic estimate (Pollock et al., 2002; Rosenberg and Kumar, 2001; Zwickl and Hillis, 2002).”
• The phylogeny and classification of post-Palaeozoic echinoids (2010, background): “Mitchell et al . 2000 ; Rosenberg & Kumar 2001 ) On the other hand, sparse sampling also has its problems and the dangers of focusing on just a small number of ‘model’ organisms to derive phylogenetic hypotheses have been highlighted by Zwickl & Hillis (2002) and Hillis et al .”
• Taxon sampling and the accuracy of phylogenetic analyses (2008, methodology): “Pollock et al. (2002) reanalyzed the Rosenberg and Kumar (2001) data using a different approach to summarizing results (measurement of error), and Zwickl and Hillis (2002) re-conducted the Rosenberg and Kumar (2001) study with a different approach to study design that examined a fuller spectrum of…”
• Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, background): “The above observations have led to a debate on whether it is preferable to sample more characters or more taxa in order to increase phylogenetic accuracy (e.g., Pollock et al. 2002, Rosenberg & Kumar 2001, Zwickl & Hillis 2002).”
• MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. (2011, methodology): “1 in Rosenberg and Kumar 2001).”
• Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers (2009, background): “Some researchers argue that obtaining longer sequence lengths or sampling more genes can compensate for potential biases due to limited taxon sampling, though this matter remains controversial ( Rosenberg and Kumar, 2001; Zwickl and Hillis, 2002; Rokas and Carroll, 2005).”