ArticleMolecular biology and evolution2012
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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86 citing papers in PubMed.
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- A taxon-rich and genome-scale phylogeny of Opisthokonta.PLoS biology · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
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- Six-State Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses.Systematic biology · 2021Article
- A genome-scale phylogeny of the kingdom Fungi.Current biology : CB · 2021Article
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- Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform.3 Biotech · 2021Article
- Evolutionary relationships of Metchnikovella dogieli Paskerova et al., 2016 (Microsporidia: Metchnikovellidae) revealed by multigene phylogenetic analysis.Parasitology research · 2021Article
- The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition.Open biology · 2021Review
- Releasing uncurated datasets is essential for reproducible phylogenomics.Nature ecology & evolution · 2020Article
- Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition.Genome biology and evolution · 2020Article
- Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter.Nature communications · 2020Article
26 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
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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