ABSTRACT
From the first phylogenetic tree, drawn by Darwin in 1837, until the late twentieth century, all of the phylogenetic trees that were constructed were composed of branches that only intersected with one another at a node or bifurcation, assuming that all genes were inherited vertically from parents to progeny, or mother cells to daughter cells. Thus, the trees resembled ordinary physical trees (Figure 15.1). However, beginning in the 1940s, examples of pieces of DNA that could move from one organism to another were discovered, generally known as horizontal gene transfer (HGT). Some of the pieces remained separate from the chromosomes (e.g., plasmids), whereas others integrated into the chromosomes (e.g., prophage and human immunodeficiency virus). These pieces often had patterns of inheritance that differed from standard patterns of inheritance. Additionally, many species import fragments of environmental DNA from dead organisms and integrate the fragments into their genomes (Figure 15.2). Although some of the fragments may have originated in individuals of the same species, most often the DNA fragments are from dissimilar species. For example, species of Archaea and Thermotogales often are found living together in hot pools. When the genomes of species of Thermotoga have been analyzed, from 9% to 11% of the genes are from species of Archaea that have been imported into the Thermotoga genomes. Up to 90% of the genomes of some dinoflagellates consist of genes from foreign sources.
