ArticleMolecular biology and evolution2012
A consistent phylogenetic backbone for the fungi.
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 56 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
56 citing papers in PubMed, 143 citations in OpenAlex.
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- A genome-scale phylogeny of the kingdom Fungi.Current biology : CB · 2021Article
- An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.Life (Basel, Switzerland) · 2020Review
- Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota).IMA fungus · 2020Article
- Fungal evolution: cellular, genomic and metabolic complexity.Biological reviews of the Cambridge Philosophical Society · 2020Article
- The modular nature of protein evolution: domain rearrangement rates across eukaryotic life.BMC evolutionary biology · 2020Article
- Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships.Systematic biology · 2020Article
- Anaerobic Fungi: Past, Present, and Future.Frontiers in microbiology · 2020Review
- Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Resolution of deep divergence of club fungi (phylum Basidiomycota).Synthetic and systems biotechnology · 2019Article
- The role of Lactobacillus species in the control of Candida via biotrophic interactions.Microbial cell (Graz, Austria) · 2019Review
- Enzymes of early-diverging, zoosporic fungi.Applied microbiology and biotechnology · 2019Review
- Airborne microbial transport limitation to isolated Antarctic soil habitats.Nature microbiology · 2019Article
- Pathogenicity patterns of mucormycosis: epidemiology, interaction with immune cells and virulence factors.Medical mycology · 2019Review
- Evolutionary Histories of Type III Polyketide Synthases in Fungi.Frontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
7 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.