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 (HGT), 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.
Three domains of life
The three main early branches of the tree of life have been intensively studied by microbiologists because the first organisms were microorganisms. Microbiologists (led by Carl Woese) have introduced the term domain for the three main branches of this tree, where domain is a phylogenetic term similar in meaning to biological kingdom. To reconstruct this tree of life, the gene sequence encoding the small subunit of ribosomal RNA (SSU rRNA, 16s rRNA) has proven useful, and the tree (as shown in the picture) relies heavily on information from this single gene.
These three domains of life represent the main evolutionary lineages of early cellular life and currently include Bacteria, Archaea (single-celled organisms superficially similar to bacteria), and Eukarya. Eukarya includes only organisms having a well-defined nucleus, such as fungi, protists, and all organisms in the plant and animals kingdoms (see figure).
The gene most commonly used for constructing phylogenetic relationships in microorganisms is the small subunit ribosomal RNA gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet variable enough that differences can be measured.
The SSU rRNA as a measure of evolutionary distances was pioneered by Carl Woese when formulating the first modern "tree of life", and his results led him to propose the Archaea as a third domain of life. However, recently it has been argued that SSU rRNA genes can also be horizontally transferred. Although this may be rare, this possibility is forcing scrutiny of the validity of phylogenetic trees based on SSU rRNAs.
Recent discoveries of "rampant" HGT in microorganisms, and the detection of horizontal movement of even genes for the small subunit of ribosomal RNA, have forced biologists to question the accuracy of at least the early branches in the tree, and even question the validity of trees as useful models of how early evolution occurs. In fact, early evolution is considered to have occurred starting from a community of progenotes, able to exchange large molecules when HGT was the standard. This lateral gene transfer occurred also beyond the Darwinian threshold, after heredity or vertical gene transfer was established. "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes." HGT is thus a potential confounding factor in inferring phylogenetic trees from the sequence of one gene. For example, if two distantly related bacteria have exchanged a gene, a phylogenetic tree including those species will show them to be closely related even though most other genes have diverged substantially. For this reason it is important to use other information to infer phylogenies, such as the presence or absence of genes, or, more commonly, to include as wide a range of genes for analysis as possible.