Chapter 22 described how, through the process of speciation, ancestral lineages divide into descendant lineages, and it is those speciation events that are captured by the branches in the tree of life. However, there are also processes of lateral gene transfer, which allow individual genes, organelles, or fragments of genomes to move horizontally from one lineage to another. Some species may pick up fragments of DNA directly from the environment. Other genes may be picked up in a viral genome and transferred to a new host when the virus becomes integrated into the new host’s genome. Hybridization between species also results in the transfer of large numbers of genes.

Lateral gene transfer can be highly advantageous to a species that incorporates novel genes from a distant relative. Genes that confer antibiotic resistance, for example, are commonly transferred among different species of bacteria. Lateral gene transfer is another way, in addition to mutation and recombination, in which species can increase their genetic variation. That genetic variation then provides the raw material on which selection acts, resulting in evolution.

A phylogenetic tree constructed from a single laterally transferred genome fragment is likely to reflect only the evolutionary history of that fragment, rather than the overall organismal phylogeny (see Key Concept 25.1). Most biologists prefer to build trees from large samples of genes or their products, so that the underlying species tree (as well as any lateral gene transfer events) can be reconstructed. Depictions of lateral gene transfer events on the underlying species tree are known as reticulations.

The degree to which lateral gene transfer events occur in various parts of the tree of life is a matter of considerable current investigation and debate. Lateral gene transfer appears to be relatively uncommon among most eukaryote lineages, although the two major endosymbioses that gave rise to mitochondria and chloroplasts can be viewed as lateral transfers of entire bacterial genomes to the eukaryote lineage. Some groups of eukaryotes, most notably some plants, are subject to relatively high levels of hybridization among closely related species. Hybridization leads to the exchange of many genes among recently separated lineages of plants. The greatest degree of lateral transfer, however, appears to occur among bacteria. Many bacterial genes have been transferred repeatedly among lineages of bacteria, to the point that relationships among bacterial species are often hard to decipher. Nonetheless, the broad relationships of the major groups of bacteria can still be determined (as we will discuss in Part Seven of this book). Lateral transfer of genes also makes it difficult to identify the boundaries of bacterial species, which is one reason why fewer bacterial species have been named than are known to exist.