Prokaryotes are a great example of horizontal gene transfer, which is the movement of genes from one species of cell to another. The most obvious warning signs are sequences that can be easily identified as having originated from viruses; the word "bacteriophages" refers to viruses that infect bacteria.

The reproductive and metabolic processes of host cells are being exploited as parasites by tiny genetically modified particles that are known as viruses. Even though they are not living cells, they frequently serve in the role of gene carriers. A virus will reproduce in one cell, emerge from that cell with a protective covering when it has finished replicating, and then enter and infect another cell during the process. This second cell can be of the same species as the first cell or of a different species. Either as a separate intracellular DNA fragment known as a plasmid or as a sequence inserted into the cell's normal genome, the viral DNA may occasionally survive in its host for many cell generations as a relatively harmless passenger. This can occur either as a plasmid, which is an intracellular DNA fragment, or as a sequence. In most cases, the tremendous expansion of virus particles within an infected cell is enough to cause the cell's death. During their journeys, viral particles have the potential to inadvertently transfer DNA pieces from one host cell's genome to the genome of another host cell. This sort of exchange of genetic material takes place regularly in prokaryotes.

On the other hand, transfers of genes in a horizontal direction take place between different bacterial species at a substantially higher frequency. A remarkable trait shared by many prokaryotes, which allows them to collect the genetic information contained in non-viral DNA molecules from their environment, is the capacity to absorb these molecules. In nature, bacteria and archaea can quite easily acquire genes from neighboring cells through either this approach or by virus-mediated transfer of genetic material. Genes that provide antibiotic resistance or the ability to produce a toxin, for example, are capable of being passed from one species of bacteria to another, where they confer a selection advantage on the recipient bacteria. In this way, it has been discovered that new strains of bacteria, some of which are potentially lethal, can emerge from the bacterial ecosystems that are found in hospitals or the many niches that exist within the human body. For instance, horizontal gene transfer is to blame for the rise in prevalence of penicillin-resistant strains of Neisseria gonorrhoeae over the past four decades. This bacteria is the causative agent of gonorrhea. On a bigger scale in terms of time, the results can be even more striking; it is estimated that at least 18% of all genes in E. coli's current genome were acquired through horizontal transfer from another species within the previous 100 million years. This occurred within the past century.

A phenomenon known to each and every one of us called sex has some similarities to the process of horizontal gene transfer that occurs among prokaryotes. In addition to the typical process of vertical transmission of genetic material from parents to offspring, the process of sexual reproduction also results in a significant horizontal transfer of genetic information between two initially distinct cell lineages, namely those of the mother and the father. One of the most important aspects of sex is undoubtedly the fact that the transmission of genetic material normally only occurs between individuals of the same species.

Even though it does not always occur, sexual reproduction is quite prevalent, particularly among eukaryotic organisms. Even bacteria are capable of engaging in carefully regulated sexual reproduction with other members of their own species on rare occasions. Natural selection has unequivocally shown a preference for species that have the capacity to reproduce sexually, despite the fact that evolutionary theorists cannot agree on the precise source of this selective advantage.

Not only are there historical reasons for the importance of family links among genes, but also the fact that they make it simpler to comprehend gene functions makes them significant. A scientist can use a computer to search the complete database of known gene sequences for genes that are related to a newly discovered gene once they have determined its sequence. This can be done by scanning the database. In a great number of instances, the roles of one or more of these homologs will already have been established through experimental research. Because the sequence of a gene is what determines its function, it is frequently possible to make an educated guess about the function of a new gene by assuming that it will be similar to the function of previously discovered homologs. We might be able to decipher a significant chunk of an organism's biology if we investigate the DNA sequence of its genome and combine that knowledge with what we already know about the functions of genes in other species of animals that have been subjected to more in-depth examination.

When we have the complete genome sequences of species that are representative of all three domains — archaea, bacteria, and eukaryotes — we are in a position to look for homologies that cut across this enormous gap in evolutionary history in a methodical manner. If we take this technique, we could start to determine the ancestry that all living things share in common. This endeavor faces a number of serious obstacles. Individual species, for instance, have regularly lost a portion of their ancestral DNA. Other genes have almost certainly been acquired via horizontal transfer from another species and are therefore not truly ancestral, despite the fact that they are shared. In point of fact, comparisons of genomes make it abundantly clear that, at least among prokaryotes, the process of evolution has been driven primarily by a combination of lineage-specific gene loss and horizontal gene transfer, with the latter occurring in some instances between evolutionarily distinct taxa. Finally, over a period of two or three billion years, some genes that were originally shared will have undergone so many changes that they can no longer be recognized.

It would appear that just a small portion of ancestral gene families have been uniformly kept in a form that can be recognized as a direct consequence of all of these peculiarities that have arisen as a result of evolution. Therefore, only 63 of the 4873 protein-coding gene families that were discovered by comparing the genomes of 50 different bacterial species, 13 different archaea, and 3 unicellular eukaryotic species are truly ubiquitous. This was determined by examining the similarities and differences between the genomes of these organisms (i.e., found in all the genomes examined). The vast majority of these universal families are made up of components that are used in the transcription and translation processes. There is a strong chance that this is not an accurate portrayal of an ancestral gene set. One can get a better, albeit still very rough, idea of the latter by adding up the gene families that have members in several, but not necessarily all, species from the three main domains. This is how one can get a better idea of the latter. This analysis uncovered 264 historical families that had been preserved over the centuries. A distinct function can be assigned to each family (typically with greater specificity, at least in terms of general biochemical activity).