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Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
Open accessAbstract
Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses.
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Citations
Cites
Hall, T. A. (1999) · Nucleic Acids Symposium Series · doi:10.14601/phytopathol_mediterr-14998u1.29 · Cited by 38,156
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,923
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,681
Tree View: An application to display phylogenetic trees on personal computers
Page, R. (1996) · Computer applications in the biosciences · doi:10.1093/bioinformatics/12.4.357 · Cited by 10,223
ExPASy: the proteomics server for in-depth protein knowledge and analysis
Gasteiger, E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg563 · Cited by 5,602
MOLECULAR BIOLOGY AND EVOLUTION
(2021) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789811250378_0003 · Cited by 4,434
Atlas of protein sequence and structure
Chang, M.-Y., Dayhoff, M. O., Eck, R. V., & Sochard, M. R. (1965) · NASA Technical Reports Server (NASA) · Cited by 4,383
Research works printed but not linked: 10
- 2820, The Journal of eukaryotic microbiology, 52, 399
- Bridge, 1995, Molecular Biology and Evolution, 12, 679
- 1820, Nature; Physical Science (London), 452, 745
- 1989, Cladistics, 5, 164
- 1999, Nucleic Acids Symposium Series, 41, 95
- 1720, Proceedings of the Royal Society B: Biological Sciences, 276, 4261
- 2000, CANADIAN JOURNAL OF BOTANY, 78, 336
- 2920, Current biology : CB, 19, 706
- 2007, BMC evolutionary biology [electronic resource], 7, S2
- 2120, Nature; Physical Science (London), 454, 955
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Self-citation
Metadata
- Authors
- Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I.
- Affiliations
- Institut de Recerca de la Biodiversitat de la Universitat de Barcelona (ES)
- Barcelona Biomedical Research Park (ES)
- University of Oxford (GB)
- Université de Montréal (CA)
- Dalhousie University (CA)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-07-18
- Volume
- 29
- Issue
- 2
- Pages
- 531-544
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3350318
- OpenAlex
- W2150623567
- Semantic Scholar
- b16f34159cb1f408e4a2796aed3dd74c788a1ea6
- Cited by
- 169
- References
- 104
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 4 · 2023: 10 · 2022: 10 · 2021: 9 · 2020: 13 · 2019: 7 · 2018: 6 · 2017: 14 · 2016: 12 · 2015: 16 · 2014: 22 · 2013: 25 · 2012: 16
- FWCI
- 8.43
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Open Access at Essex (University of Essex) (acceptedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- Harvard University
- Broad Institute
- Institució Catalana de Recerca i Estudis Avançats
- National Institutes of Health
- National Human Genome Research Institute (U54HG003273)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Keywords
- Opisthokonta, eukaryotic phylogeny, orthology assignment, paralogy, Ichthyosporea, Choanoflagellata, animals, Blastocladiomycota, Chytridiomycota, systematic errors, cat model
- MeSH terms
- Animals, Bayes Theorem, Fungi, Models, Genetic, Phylogeny, Likelihood Functions, Sequence Alignment, Sequence Analysis, DNA, Protein Structure, Tertiary, Evolution, Molecular, Genomics, Eukaryota
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