ArticleProceedings of the National Academy of Sciences of the United States of America2010
Biased gene transfer mimics patterns created through shared ancestry.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 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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Who cites it
34 citing papers in PubMed, 56 citations in OpenAlex.
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- A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes.Scientific reports · 2020Article
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- Insights into origin and evolution of α-proteobacterial gene transfer agents.Virus evolution · 2017Article
- Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.Genome biology and evolution · 2016Article
- Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions.F1000Research · 2016Review
- Evolutionary change and phylogenetic relationships in light of horizontal gene transfer.Journal of biosciences · 2015Review
- Ancient horizontal gene transfer and the last common ancestors.BMC evolutionary biology · 2015Article
- Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.Journal of molecular evolution · 2015Article
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- Emergence and evolution.Topics in current chemistry · 2014Review
- Inteins as indicators of gene flow in the halobacteria.Frontiers in microbiology · 2014Article
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- Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past.Genome biology and evolution · 2013Article
- Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.Open biology · 2012Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In phylogenetic reconstruction, two types of bacterial tyrosyl-tRNA synthetases (TyrRS) form distinct clades with many bacterial phyla represented in both clades. Very few taxa possess both forms, and maximum likelihood analysis of the distribution of TyrRS types suggests horizontal gene transfer (HGT), rather than an ancient duplication followed by differential gene loss, as the contributor to the evolutionary history of TyrRS in bacteria. However, for each TyrRS type, phylogenetic reconstruction yields phylogenies similar to the ribosomal phylogeny, revealing that frequent gene transfer has not destroyed the expected phylogeny; rather, the expected phylogenetic signal was reinforced or even created by HGT. We show that biased HGT can mimic patterns created through shared ancestry by in silico simulation. Furthermore, in cases where genomic synteny is sufficient to allow comparisons of relative gene positions, both tyrRS types occupy equivalent positions in closely related genomes, rejecting the loss hypothesis. Although the two types of bacterial TyrRS are only distantly related and only rarely coexist in a single genome, they have many features in common with alleles that are swapped between related lineages. We propose to label these functionally similar homologs as homeoalleles. We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.
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