page_title: Horizontal gene transfer in evolution
section_title: Resolution of uncertainty with phylogenomics
hierarchical_section_title: Horizontal gene transfer in evolution / Resolution of uncertainty with phylogenomics
caption_attribution_description: English: The W-G Tree Based on the Median Tree Algorithm
context_page_description: Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer, scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.
  HGT happens very infrequently – at the individual organism level, it is highly improbable for any such event to take place. However, on the grander scale of evolutionary history, these events occur with some regularity. On one hand, this forces biologists to abandon the use of individual genes as good markers for the history of life. On the other hand, this provides an almost unexploited large source of information about the past.
context_section_description: Despite the uncertainties in reconstructing phylogenies back to the beginnings of life, progress is being made in reconstructing the tree of life in the face of uncertainties raised by HGT. The uncertainty of any inferred phylogenetic tree based on a single gene can be resolved by using several common genes or even evidence from whole genomes. One such approach, sometimes called 'multi-locus typing', has been used to deduce phylogenic trees for organisms that exchange genes, such as meningitis bacteria.
  Jonathan Eisen and Claire Fraser have pointed out that:
  "In building the tree of life, analysis of whole genomes has begun to supplement, and in some cases to improve upon, studies previously done with one or a few genes. For example, recent studies of complete bacterial genomes have suggested that the hyperthermophilic species are not deeply branching; if this is true, it casts doubt on the idea that the first forms of life were thermophiles. Analysis of the genome of the eukaryotic parasite Encephalitozoon cuniculi supports suggestions that the group Microsporidia are not deep branching protists but are in fact members of the fungal kingdom. Genome analysis can even help resolve relationships within species, such as by providing new genetic markers for population genetics studies in the bacteria causing anthrax or tuberculosis. In all these studies, it is the additional data provided by a complete genome sequence that allows one to separate the phylogenetic signal from the noise. This is not to say the tree of life is now resolved – we only have sampled a smattering of genomes, and many groups are not yet touched"
  These approaches are enabling estimates of the relative frequency of HGT; the relatively low values that have been observed suggests that the 'tree' is still a valid metaphor for evolution – but the tree is adorned with 'cobwebs' of horizontally transferred genes. This is the main conclusion of a 2005 study of more than 40 complete microbial genomic sequences by Fan Ge, Li-San Wang, and Junhyong Kim. They estimate the frequency of HGT events at about 2% of core genes per genome. Similar whole genome approaches to assessing evolution are also enabling progress in identifying very early events in the tree of life, such as a proposal that eukaryotes arose by fusion of two complete but very diverse prokaryote genomes: one from a bacterium and one from an archaeal cell.
  Such a fusion of organisms hypothesis for the origin of complex nucleated cells has been put forward by Lynn Margulis using quite different reasoning about symbiosis between a bacterium and an archaen arising in an ancient consortium of microbes.
caption: Tree Based on the Median Tree Algorithm.[9] Branches with bootstrap (statistical) scores less than 50% were collapsed. The three domains of life are (A) archaea, (B–J) bacteria, and (K) eukaryote. Species are labeled with different colors based on their inferred HGT rates: red, >4%; yellow, 3–4%; pink, 2–3%; blue, 1–2%; green, <1%. Taxonomy labels are (A) Euryarchaea, (B) Proteobacteria, (C) Chlamydiae, (D) Spirochaetes, (E) Thermotogae, (F) Aquificae, (G) Actinobacteria, (H) Deinococcus, (I) Cyanobacteria, (J) Firmicutes, and (K) Fungi.
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