The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
Open accessAbstract
Over the past two decades, there has been a long-standing debate about the impact of taxon sampling on phylogenetic inference. Studies have been based on both real and simulated data sets, within actual and theoretical contexts, and using different inference methods, to study the impact of taxon sampling. In some cases, conflicting conclusions have been drawn for the same data set. The main questions explored in studies to date have been about the effects of using sparse data, adding new taxa, including more characters from genome sequences and using different (or concatenated) locus regions. These questions can be reduced to more fundamental ones about the assessment of data quality and the design guidelines of taxon sampling in phylogenetic inference experiments. This review summarizes progress to date in understanding the impact of taxon sampling on the accuracy of phylogenetic analysis.
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Citations
Cites
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · cited 3×
“Based on the successes of studies demonstrating the feasibility of genome-scale taxa to resolve phylogenetic inference conflicts [38, 91], many studies have made use of genome-scale data to address one of the most fundamental aspirations of phylogenetic studies: to build the tree of life [2, 21, 40, 71, 92].”
BackgroundEvidence for a clade of nematodes, arthropods and other moulting animals
Aguinaldo, A. M. A., Turbeville, J. M., Linford, L. S., Rivera, M. C., Garey, J. R., Raff, R. A., & Lake, J. A. (1997) · Nature · doi:10.1038/387489a0 · Cited by 1,609
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512
A review of long-branch attraction
Bergsten, J. (2005) · Cladistics · doi:10.1111/j.1096-0031.2005.00059.x · Cited by 1,162
Phylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698
Keeling, P. J., Burger, G., Durnford, D. G., Lang, B. F., Lee, R. W., Pearlman, R. E., Roger, A. J., & Gray, M. W. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.09.005 · Cited by 579
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553
Philippe, H., Lartillot, N., & Brinkmann, H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi111 · Cited by 551
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · cited 1×
“Some phylogenetic inference methods also make use of relaxed molecular clock models that do not assume a constant rate of molecular evolution across lineages [60–62].”
MethodResolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
Hedtke, S. M., Townsend, T. M., & Hillis, D. M. (2006) · Systematic Biology · doi:10.1080/10635150600697358 · Cited by 303
Cited by
Ctenophore relationships and their placement as the sister group to all other animals
Whelan, N. V., Kocot, K. M., Moroz, T. P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L. L., & Halanych, K. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0331-3 · Cited by 263
Incongruence in the phylogenomics era
Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 259
Dai, W., Zou, M., Yang, L., Du, K., Chen, W., Shen, Y., Mayden, R. L., & He, S. (2018) · Scientific Reports · doi:10.1038/s41598-017-18432-5 · Cited by 26
Metadata
- Authors
- Nabhan, A. R., & Sarkar, I. N.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-03-23
- Volume
- 13
- Issue
- 1
- Pages
- 122-134
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W2150178057
- Cited by
- 234
- References
- 13
- FWCI
- 3.41
- Type
- journal article
- Language
- en
- Open access
- bronze
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