ArticleNature ecology & evolution2018
Gene transfers can date the tree of life.
Article in Nature ecology & evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 76 citations in OpenAlex.
- Dating the Bacterial Tree of Life Based on Ancient Symbiosis.Systematic biology · 2025Article
- A timetree of Fungi dated with fossils and horizontal gene transfers.Nature ecology & evolution · 2025Article
- Oxidative adaptations in prokaryotes imply the oxygenic photosynthesis before crown-groupPNAS nexus · 2025Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.Bioinformatics (Oxford, England) · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Adaptive radiations in natural populations of prokaryotes: innovation is key.FEMS microbiology ecology · 2023Article
- Electron transport chains as a window into the earliest stages of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DaTeR: error-correcting phylogenetic chronograms using relative time constraints.Bioinformatics (Oxford, England) · 2023Article
- virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- A consensus view of the proteome of the last universal common ancestor.Ecology and evolution · 2022Article
- Relative Time Constraints Improve Molecular Dating.Systematic biology · 2022Article
- Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.Genome biology and evolution · 2022Review
- An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.eLife · 2022Article
- Relative Time Inference Using Lateral Gene Transfers.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Dating Microbial Evolution with MCMCtree.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A Computational Protocol for Dating the Evolution of Cyanobacteria.Methods in molecular biology (Clifton, N.J.) · 2022Article
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6 authors at 3 institutions in 4 countries.
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Abstract
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya. We present the order of speciations according to lateral gene transfer data calibrated to geological time for three datasets comprising 40 genomes for Cyanobacteria, 60 genomes for Archaea and 60 genomes for Fungi. An inspection of discrepancies between transfers and clocks and a comparison with mammalian fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.
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