A5079867150- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Microbial Metabolic Engineering and Bioproduction
- Genetic diversity and population structure
- Protist diversity and phylogeny
- ATP Synthase and ATPases Research
- Mitochondrial Function and Pathology
- Photosynthetic Processes and Mechanisms
- Evolution and Paleontology Studies
- Chromosomal and Genetic Variations
- Probiotics and Fermented Foods
- Evolution and Genetic Dynamics
- Scientific Computing and Data Management
- Mycorrhizal Fungi and Plant Interactions
- CRISPR and Genetic Engineering
- Agricultural Engineering and Mechanization
- Food composition and properties
- Agricultural Economics and Practices
- Seed and Plant Biochemistry
- Geology and Paleoclimatology Research
- Sunflower and Safflower Cultivation
- Crop Yield and Soil Fertility
- Plant-Microbe Interactions and Immunity
- Genome Rearrangement Algorithms
- RNA and protein synthesis mechanisms
The University of Tokyo
2023-2024
The University of Queensland
2020-2023
Tokyo University of Science
2023
RIKEN Center for Advanced Intelligence Project
2020
Eötvös Loránd University
2018-2019
Université Claude Bernard Lyon 1
2015-2018
Centre National de la Recherche Scientifique
2017-2018
Laboratoire de Biométrie et Biologie Evolutive
2015-2018
Institut National de la Recherche Agronomique
1983
École Nationale d'Ingénieurs des Techniques des Industries Agro-Alimentaires
1983
A rooted bacterial tree is necessary to understand early evolution, but the position of root contested. Here, we model evolution 11,272 gene families identify root, extent horizontal transfer (HGT), and nature last common ancestor (LBCA). Our analyses between major clades Terrabacteria Gracilicutes suggest that LBCA was a free-living flagellated, rod-shaped double-membraned organism. Contrary recent proposals, our reject basal placement Candidate Phyla Radiation, which instead branches...
Abstract The timing of early cellular evolution, from the divergence Archaea and Bacteria to origin eukaryotes, is poorly constrained. ATP synthase complex thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. We reconstruct evolutionary history synthases using an expanded taxon sampling set develop phylogenetic cross-bracing approach, constraining equivalent speciation nodes be...
Although the role of lateral gene transfer is well recognized in evolution bacteria, it generally assumed that has had less influence among eukaryotes. To explore this hypothesis, we compare dynamics genome two groups organisms: cyanobacteria and fungi. Ancestral genomes are inferred both clades using types methods: first, Count, a tree unaware method models duplications, gains losses to explain observed numbers genes present genome; second, ALE, more recent tree-aware reconciles trees with...
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea microbial eukaryotes prevented a comprehensive dating tree life. Here, we show that patterns lateral gene transfer deduced an analysis modern genomes encode novel abundant source information about temporal coexistence lineages throughout history We use state-of-the-art species tree-aware phylogenetic methods to reconstruct thousands families demonstrate dates implied by transfers are...
Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for first time extinct lineages. It also incorporates various features have not date been combined single simulator, such as possibility generating species trees with pre-defined variation speciation extinction rates through time, simulating explicitly intergenic variable length outputting gene tree-species tree reconciliations.Source code manual are freely available...
Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding evolution in deep time. However, the co-evolution life Earth system signatures bacterial metabolism geochemical most conspicuously Great Oxidation Event (GOE) ∼2.33 billion years ago (Ga, (Poulton et al. 2021)), which oxygenic photosynthesis tectonism (Eguchi, Seales, Dasgupta 2019) transformed Earth’s biosphere from dominantly anaerobic to aerobic. Here, we combine...
Abstract Motivation A reconciliation is an annotation of the nodes a gene tree with evolutionary events—for example, speciation, duplication, transfer, loss, etc.—along mapping onto species tree. Many algorithms and software produce or use reconciliations but often using different formats, regarding type events considered whether dated not. This complicates comparison communication between programs. Results Here, we gather consortium developers in to propose endorse format that aims promote...
Abstract An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose standardized archaeal taxonomy, as part Genome Taxonomy Database (GTDB), derived 122 concatenated protein phylogeny that resolves polyphyletic groups normalizes ranks relative divergence (RED). The resulting is stable under range phylogenetic variables, including marker genes, inference...
Abstract Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including duplication, transfer and loss genes. Over past ten years these have emerged as powerful tool for inferring rooting trees, ancestral repertoires, studying processes genome evolution. However, complex can be more difficult to use than traditional approaches. Method development is rapid, it decide between approaches interpret results. Here, we...
Abstract ALE and GeneRax are tools for probabilistic gene tree–species tree reconciliation. Based on a common underlying statistical model of how trees evolve along species trees, these methods rely vs. discordance to infer duplication, transfer, loss events, map family origins, root trees. Published analyses have used Archaea, Bacteria, several eukaryotic groups, as well ancestral repertoires. However, it was recently suggested that reconciliation-based estimates duplication transfer events...
Bacteria are the most abundant and metabolically diverse cellular lifeforms on Earth. A rooted bacterial phylogeny provides a framework to interpret this diversity understand nature of early life. Inferring position root is complicated by incomplete taxon sampling long branch archaeal outgroup. To circumvent these limitations, we model genome evolution at level gene duplication, transfer loss events, allowing outgroup-free inference 1 . We infer tree which 68% transmission events vertical....
Abstract Lateral gene transfers between ancient species contain information about the relative timing of diversification. Specifically, ancestors a donor must have existed before descendants recipient species. Hence, detection transfer event can be translated into time constraint nodes phylogeny if and identified. When set is detected by interpreting phylogenetic discordance trees tree, all deduced constraints used to rank i.e. order totally its internal nodes. Unfortunately lateral...
Abstract The timing of early cellular evolution from the divergence Archaea and Bacteria to origin eukaryotes remains poorly constrained. ATP synthase complex is thought have originated prior Last Universal Common Ancestor (LUCA) analyses genes, together with ribosomes, played a key role in inferring rooting tree life. Here we reconstruct evolutionary history synthases using an expanded sampling Archaea, Bacteria, eukaryotes. We developed phylogenetic cross-bracing approach making use...
Abstract Summary Here we present Zombi , a tool to simulate the evolution of species, genomes and sequences in silico that considers for first time extinct lineages. It also incorporates various features have not date been combined single simulator, such as possibility generating species trees with pre-defined variation speciation extinction rates through time, simulating explicitly intergenic variable length outputting gene tree - reconciliations. Availability implementation Source code...
Biodiversity has always been predominantly microbial and the scarcity of fossils from bacteria, archaea eukaryotes prevented a comprehensive dating tree life. Here we show that patterns lateral gene transfer deduced analysis modern genomes encode novel abundant source information about temporal coexistence lineages throughout history We use new phylogenetic methods to reconstruct thousands families demonstrate dates implied by transfers are consistent with estimates relaxed molecular clocks...