The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
Open accessAbstract
The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.
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Cites
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463
Toward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
Dating the rise of atmospheric oxygen
Bekker, A., Holland, H. D., Wang, P.-L., Rumble, D., Stein, H. J., Hannah, J. L., Coetzee, L. L., & Beukes, N. J. (2004) · Nature · doi:10.1038/nature02260 · Cited by 1,435 · cited 1×
“32 billion years ago (Ga) (31) is attributed to cyanobacteria (32), but many details of these associations continue to be investigated (33, 34); (ii) unambiguous microfossil evidence dates to ∼2.”
BackgroundThe timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638
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
Estimating metazoan divergence times with a molecular clock
Peterson, K. J., Lyons, J. B., Nowak, K. S., Takacs, C. M., Wargo, M. J., & McPeek, M. A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401670101 · Cited by 461
Life on a young planet: the first three billion years of evolution on Earth
(2003) · Choice Reviews Online · doi:10.5860/choice.41-2190 · Cited by 442
An early-branching microbialite cyanobacterium forms intracellular carbonates
Couradeau, E., Benzerara, K., Gérard, E., Moreira, D., Bernard, S., Brown, G. E., & López-García, P. (2012) · Science · doi:10.1126/science.1216171 · Cited by 263
Benton, M. J., & Ayala, F. J. (2003) · Science · doi:10.1126/science.1077795 · Cited by 252
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Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature · doi:10.1038/nature12352 · Cited by 2,394
Superoxide dismutases and superoxide reductases
Sheng, Y., Abreu, I. A., Cabelli, D. E., Maroney, M. J., Miller, A.-F., Teixeira, M., & Valentine, J. S. (2014) · Chemical Reviews · doi:10.1021/cr4005296 · Cited by 1,081
PhyloSift: phylogenetic analysis of genomes and metagenomes
Darling, A. E., Jospin, G., Lowe, E., Matsen, F. A., Bik, H. M., & Eisen, J. A. (2014) · PeerJ · doi:10.7717/peerj.243 · Cited by 631
An archaeal origin of eukaryotes supports only two primary domains of life
Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013) · Nature · doi:10.1038/nature12779 · Cited by 519
Unraveling the processes shaping mammalian gut microbiomes over evolutionary time
Groussin, M., Mazel, F., Sanders, J. G., Smillie, C. S., Lavergne, S., Thuiller, W., & Alm, E. J. (2017) · Nature Communications · doi:10.1038/ncomms14319 · Cited by 508
Metadata
- Authors
- Szöllősi, G. J., Boussau, B., Abby, S. S., Tannier, E., & Daubin, V.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-10-04
- Volume
- 109
- Issue
- 43
- Pages
- 17513-17518
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2138113680
- Cited by
- 194
- References
- 11
- FWCI
- 6.62
- Type
- journal article
- Language
- en
- Open access
- green
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