ReviewThe ISME journal2024
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.
Review in The ISME journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- DVE-1 is a telomere-binding protein and links the NuRD complex to telomere regulation iniScience · 2026Article
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Ancestral gene content estimates under gain-loss-duplication depend on the chosen observation threshold.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- New lineages provide insights into the convergent evolution of extreme salt adaptation within symbiotic Archaea.Molecular biology and evolution · 2026Article
- AliFilter: a machine learning approach to alignment filtering.Molecular biology and evolution · 2026Article
- Toward a genomic understanding of the tree of life.Molecular biology and evolution · 2026Article
- GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.Nucleic acids research · 2026Article
- Review
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- A timetree of Fungi dated with fossils and horizontal gene transfers.Nature ecology & evolution · 2025Article
- Dynamic Changes in the Crop Milk and Salivary Microbiota of Breeding Pigeons During the Raising Brooding Period.Animals : an open access journal from MDPI · 2025Article
- Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.Molecular biology and evolution · 2025Article
- DPANN Archaea and CPR Bacteria: insights into early cellular evolution?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- The emergence of metabolisms through Earth history and implications for biospheric evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.ISME communications · 2025Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.