The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Dealing with incongruence in phylogenomic analyses
Open accessAbstract
Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent. We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Prokaryotic Evolution in Light of Gene Transfer
Gogarten, J. P., Doolittle, W. F., & Lawrence, J. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004046 · Cited by 986
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
Natural history and evolutionary principles of gene duplication in fungi
Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A. (2007) · Nature · doi:10.1038/nature06107 · Cited by 614
Pattern pluralism and the Tree of Life hypothesis
Doolittle, W. F., & Bapteste, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610699104 · Cited by 546
Highways of gene sharing in prokaryotes
Beiko, R. G., Harlow, T. J., & Ragan, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504068102 · Cited by 535
Does a tree–like phylogeny only exist at the tips in the prokaryotes?
Creevey, C. J., Fitzpatrick, D. A., Philip, G. K., Kinsella, R. J., O'Connell, M. J., Pentony, M. M., Travers, S. A., Wilkinson, M., & McInerney, J. O. (2004) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2004.2864 · Cited by 126
Cited by
Horizontal gene transfer in evolution: facts and challenges
Boto, L. (2010) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2009.1679 · Cited by 379
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe-Fadrosh, E. A., Meier-Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Paez-Espino, D., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3886 · Cited by 267
How stands the Tree of Life a century and a half after The Origin?
O'Malley, M. A., & Koonin, E. V. (2011) · Biology Direct · doi:10.1186/1745-6150-6-32 · Cited by 106
Nagy, L. G., Riley, R., Bergmann, P. J., Krizsán, K., Martin, F. M., Grigoriev, I. V., Cullen, D., & Hibbett, D. S. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msw238 · Cited by 90
Doolittle, W. F. (2009) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0032 · Cited by 76
Metadata
- Authors
- Galtier, N., & Daubin, V.
- Venue
- Philosophical Transactions of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2008-10-07
- Volume
- 363
- Issue
- 1512
- Pages
- 4023-4029
- ISSN
- 0962-8436 (ISSN-L)
- 1471-2970
- OpenAlex
- W2082473664
- Cited by
- 272
- References
- 7
- FWCI
- 6.33
- Type
- journal article
- Language
- en
- Open access
- green
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