Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates

Stanhope, Michael J.; Lupas, Andrei N.; Italia, Michael J.; Koretke, Kristin K.; Volker, Craig; Brown, James R.

doi:10.1038/35082058

Cited by 206 publications

(130 citation statements)

References 15 publications

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“…7-10), yet HGT is thought to be infrequent in multicellular organisms (11)(12)(13). This is because multicellular organisms often separate their germ-line cells from their somatic cells, so the reproductive genome is in part isolated from contact with foreign sources of DNA.…”

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confidence: 99%

A tale of two tardigrades

Richards

Monier

2016

Proc. Natl. Acad. Sci. U.S.A.

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confidence: 99%

A tale of two tardigrades

Richards

Monier

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…68 ). Orthology assessment ideally requires rigorous and time-consuming phylogenetic analyses of individual genes 47,69,70 . showed only a limited effect of these factors on the results 52,54 .…”

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confidence: 99%

Phylogenomics and the reconstruction of the tree of life

2005

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Correspondence to H.P. email: herve.philippe@umontreal.ca -2 - PrefaceAs more complete genomes are sequenced, phylogenetic analysis is entering a new era -that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms based on the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to a number of fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life may prove difficult, if not impossible, to resolve with confidence. Introductory paragraphUnderstanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. The notion of phylogeny follows directly from the theory of evolution presented by Charles Darwin in "The Origin of Species" 1 : the only illustration in his famous book is the first representation of evolutionary relationships among species, in the form of a phylogenetic tree. The subsequent enthusiasm of biologists for the phylogenetic concept is illustrated by the publication of Ernst Haeckel's famous "trees" as early as 1866 2 .Today, phylogenetics -the reconstruction of evolutionary history -relies on using mathematical methods to infer the past from features of contemporary species, with only the fossil record to provide a window on the evolutionary past of life on our planet. This reconstruction involves the identification of HOMOLOGOUS CHARACTERS that are shared among different organisms, and the inference of phylogenetic trees from the comparison of these characters using reconstruction methods (BOX 1). The accuracy of -3 -the inference is therefore heavily dependent upon the quality of models for the evolution of such characters. Because the underlying mechanisms are not yet well understood, reconstructing the evolutionary history of life on Earth based solely on the information provided by living organisms has turned out to be difficult.Until the 1970s, which brought the dawn of molecular techniques for sequencing proteins and DNA, phylogenetic reconstruction was essentially based on the analysis of morphological or ultrastructural characters. The comparative anatomy of fossils and extant species has proved powerful in some respects; for example, the main groups of animals and plants have been delineated fairly easily using these methods. However, this approach is hampered by the limited number of reliable homologous characters available; these are almost non-existent in micro-organisms 3 and are rare even in complex organisms.The introduction of the use of molecular data in phylogenetics 4 led to a revolution.In the late 1980s, access to DNA sequences increased the number of homologous characters that could be compared from less than 100 to more than 1,000, ...

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“…Indeed, outright lateral gene transfer from bacterial donors to eukaryotes has become a popular explanatory principle (26). Even the human genome was initially claimed to contain hundreds of such bacterial acquisitions (27), but closer inspection by experienced eyes revealed that those claims for rampant lateral transfer to humans were premature (28,29). Given that lateral gene transfer (LGT) claims are usually founded in gene phylogenies (26), and given that gene phylogenies have severe limitations (30), it seems prudent to ask: Just how good is the evidence for rampant LGT from food (or other) bacteria to eukaryotic nuclei as opposed to the evidence for transfers from organelles?…”

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confidence: 99%