ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2015
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 111 citations in OpenAlex.
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review.World journal of microbiology & biotechnology · 2026Review
- Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.Molecular biology and evolution · 2025Article
- Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.Molecular biology and evolution · 2025Article
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- Article
- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
- Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.Science advances · 2024Article
- Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution.Molecular biology and evolution · 2024Article
- Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes.Genome biology and evolution · 2024Article
- The nature of the last universal common ancestor and its impact on the early Earth system.Nature ecology & evolution · 2024Article
- Gene Transfer Among Viruses Substantially Contributes to Gene Gain of Giant Viruses.Molecular biology and evolution · 2024Article
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets.Molecular biology and evolution · 2023Article
- Wood-Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history.mSystems · 2023Article
- Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.Genome biology and evolution · 2023Article
- Article
- The evolution of morphological development is congruent with the species phylogeny in the genusFrontiers in microbiology · 2023Article
- Gene gain facilitated endosymbiotic evolution of Chlamydiae.Nature microbiology · 2023Article
- Comparative Genomic Insights into the Evolution ofmSystems · 2022Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.
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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.