The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Open accessAbstract
An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level "supergroups," many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup "Chromalveolata" is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.
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Cites
ProtTest: selection of best-fit models of protein evolution
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“The second approach was to use Concaterpillar to identify protein-coding genes with discordant histories (Leigh et al. 2008), which could be caused by EGT or LGT. Repeated runs yielded different results, indicating an absence of supported discordances.”
InfluentialPhylogenomics: The beginning of incongruence?
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Taxon sampling and the accuracy of phylogenetic analyses
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Genomic footprints of a cryptic plastid endosymbiosis in diatoms
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Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling
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Cited by
The Revised Classification of Eukaryotes
Adl, S. M., Simpson, A. G. B., Lane, C. E., Lukeš, J., Bass, D., Bowser, S. S., Brown, M. W., Burki, F., Dunthorn, M., Hampl, V., et al. (2012) · Journal of Eukaryotic Microbiology · doi:10.1111/j.1550-7408.2012.00644.x · Cited by 1,680
Self-citationEstimating the timing of early eukaryotic diversification with multigene molecular clocks
Parfrey, L. W., Lahr, D. J. G., Knoll, A. H., & Katz, L. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110633108 · Cited by 899
Self-citationAnchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012) · Systematic Biology · doi:10.1093/sysbio/sys049 · Cited by 833
On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
Eme, L., Sharpe, S. C., Brown, M. W., & Roger, A. J. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016139 · Cited by 287
Genome-reconstruction for eukaryotes from complex natural microbial communities
West, P. T., Probst, A. J., Grigoriev, I. V., Thomas, B. C., & Banfield, J. F. (2018) · Genome Research · doi:10.1101/gr.228429.117 · Cited by 266
Metadata
- Authors
- Parfrey, L. W., Grant, J., Tekle, Y. I., Lasek-Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-07-23
- Volume
- 59
- Issue
- 5
- Pages
- 518-533
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2163525789
- Cited by
- 231
- References
- 12
- FWCI
- 15.36
- Type
- journal article
- Language
- en
- Open access
- green
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- Parfrey, L. W., Grant, J., Tekle, Y. I., Lasek-Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A. (2010). Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life. Systematic Biology. https://doi.org/10.1093/sysbio/syq037
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