ArticleMobile genetic elements2011
HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion.
Article in Mobile genetic elements, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).Ecology and evolution · 2024Article
- Rates of gene conversions between Escherichia coli ribosomal operons.G3 (Bethesda, Md.) · 2021Article
- The Complete Mitogenome ofFrontiers in plant science · 2021Article
- Ankyrin domain encoding genes from an ancient horizontal transfer are functionally integrated into Nasonia developmental gene regulatory networks.Genome biology · 2018Article
- Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses.Molecular biology and evolution · 2017Article
- Extensive horizontal gene transfers between plant pathogenic fungi.BMC biology · 2016Article
- Public health evolutionary biology of antimicrobial resistance: priorities for intervention.Evolutionary applications · 2015Article
- Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.G3 (Bethesda, Md.) · 2014Article
- Article
- Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae).Genome biology and evolution · 2013Article
- Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis.Genome biology and evolution · 2013Article
- Revisiting bacterial phylogeny: Natural and experimental evidence for horizontal gene transfer of 16S rRNA.Mobile genetic elements · 2013Article
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When "duplicative HGT" introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term "HGT turbulence" to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.
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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.