ArticleGenome research2005
The net of life: reconstructing the microbial phylogenetic network.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed, 265 citations in OpenAlex.
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- Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.Journal of the Royal Society, Interface · 2021Article
- Comparative analysis of integrative and conjugative mobile genetic elements in the genusMicrobial genomics · 2021Article
- An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.Genome biology and evolution · 2021Article
- Timing the evolution of antioxidant enzymes in cyanobacteria.Nature communications · 2021Article
- Ancestral state reconstruction of metabolic pathways across pangenome ensembles.Microbial genomics · 2020Article
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- Understanding Horizontal Gene Transfer network in human gut microbiota.Gut pathogens · 2020Article
- Implications of Mobile Genetic Elements forApplied and environmental microbiology · 2019Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the "net of life". We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as "vines", and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.
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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.