Faculty Opinions recommendation of Ancient horizontal gene transfer can benefit phylogenetic reconstruction.

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

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Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction

Horizontal Gene Transfer - Methods in Molecular Biology ◽

10.1007/978-1-60327-853-9_14 ◽

2009 ◽

pp. 241-256 ◽

Cited By ~ 15

Author(s):

Robert G. Beiko ◽

Mark A. Ragan

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Reconstruction

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Ancient horizontal gene transfer can benefit phylogenetic reconstruction

Trends in Genetics ◽

10.1016/j.tig.2006.05.004 ◽

2006 ◽

Vol 22 (7) ◽

pp. 361-366 ◽

Cited By ~ 52

Author(s):

J HUANG ◽

J GOGARTEN

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Reconstruction

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ShadowCaster: compositional methods under the shadow of phylogenetic models for the detection of horizontal gene transfer events in prokaryotes

10.1101/684704 ◽

2019 ◽

Author(s):

Daniela Sánchez-Soto ◽

Guillermin Agüero-Chapin ◽

Vinicio Armijos-Jaramillo ◽

Yunierkis Perez-Castillo ◽

Eduardo Tejera ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Hybrid Approach ◽

Phylogenetic Reconstruction ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Computational Approaches ◽

Link Type ◽

Reconstruction Methods ◽

Phylogenetic Models

AbstractHorizontal gene transfer (HGT) plays an important role in the evolution of many organisms, especially in prokaryotes where commonly occurs. Microbial communities can improve survival due to the evolutionary innovations induced by HGT events. Thus, several computational approaches have arisen to identify such events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. On the other hand, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to genomic scale, however, they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines compositional features under the shadow of phylogenetic models independent of tree reconstruction to improve the detection of HTG events in prokaryotes. ShadowCaster predicted successfully close and distant HTG events in both artificial and bacterial genomes. It detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches. ShadowCaster’s predictions showed the highest agreement among those obtained with other assayed methods. ShadowCaster is released as an open-source software under the GPLv3 license. Source code is hosted at https://github.com/dani2s/ShadowCaster and documentation at https://shadowcaster.readthedocs.io/en/latest/.

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