ArticleProceedings of the National Academy of Sciences of the United States of America2005
Decoding the genomic tree of life.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Decision Making in Plants: A Rooted Perspective.Plants (Basel, Switzerland) · 2023Article
- To assemble or not to resemble-A validated Comparative Metatranscriptomics Workflow (CoMW).GigaScience · 2019Article
- Chromosome architecture constrains horizontal gene transfer in bacteria.PLoS genetics · 2018Article
- Enrichment of bacterial DNA for the diagnosis of blood stream infections.BMC infectious diseases · 2016Article
- Eukaryotic origins.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Review
- HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.BMC genomics · 2014Article
- Article
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
- Rooting gene trees without outgroups: EP rooting.Genome biology and evolution · 2012Article
- A rooted net of life.Biology direct · 2011Article
- How stands the Tree of Life a century and a half after The Origin?Biology direct · 2011Review
- Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes.Proceedings. Biological sciences · 2011Article
- Archaea--timeline of the third domain.Nature reviews. Microbiology · 2011Review
- Article
- Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation.PloS one · 2010Article
- How much of protein sequence space has been explored by life on Earth?Journal of the Royal Society, Interface · 2008Article
- Concerted gene recruitment in early plant evolution.Genome biology · 2008Article
- Hybrid vigor between native and introduced salamanders raises new challenges for conservation.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Article
- Enzyme-driven speciation: crystallizing Archaea via lipid capture.Journal of molecular evolution · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic tree of 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.