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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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The Revised Classification of Eukaryotes
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Naranjo-Ortíz, M. A., & Gabaldón, T. (2019) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12550 · Cited by 401
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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