ArticleBiology direct2011
A rooted net of life.
Article in Biology direct, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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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.
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Who cites it
19 citing papers in PubMed.
- Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta.Scientific reports · 2021Article
- Article
- The Landscape of the Emergence of Life.Life (Basel, Switzerland) · 2017Article
- Horizontal gene transfer: building the web of life.Nature reviews. Genetics · 2015Review
- Microorganisms-A Journal and a Unifying Concept for the Science of Microbiology.Microorganisms · 2014Article
- Article
- Transfer of noncoding DNA drives regulatory rewiring in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Bacterial genome instability.Microbiology and molecular biology reviews : MMBR · 2014Review
- Review
- Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12.Applied and environmental microbiology · 2013Article
- EGN: a wizard for construction of gene and genome similarity networks.BMC evolutionary biology · 2013Article
- Molecular paleontology: a biochemical model of the ancestral ribosome.Nucleic acids research · 2013Article
- Quartet decomposition server: a platform for analyzing phylogenetic trees.BMC bioinformatics · 2012Article
- The role of reticulate evolution in creating innovation and complexity.International journal of evolutionary biology · 2012Article
- Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales.Genome biology and evolution · 2012Article
- Phylogenomics of prokaryotic ribosomal proteins.PloS one · 2012Article
- Quantifying homologous replacement of loci between haloarchaeal species.Genome biology and evolution · 2012Article
- Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.Frontiers in cellular and infection microbiology · 2012Review
- Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.Biology direct · 2011Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages.
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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.