Though often much more elaborate in practice, nonetheless sexual processes have two key components, outcrossing and recombination. Outcrossing is another way of saying that the genetic material involved in the subsequent recombination process has been sourced from two different parents and, in terms of genetic variability, from two more rather than less genetically distinct individuals. Mechanisms of recombination can vary, and this variation can impact the likelihood that recombination will follow outcrossing (see Recombination). In this section I focus on differences in mechanisms of outcrossing. Subsequently I consider differences in the likelihood of survival of recombinative products in the face of natural selection. That is, sex may in fact be viewed as a three-step process: outcrossing that is followed by genetic recombination which in turn is followed by natural selection acting on the resulting recombinant genotype (or even four: outcrossing → pre-genetic recombination state → recombination → natural selection, where outcrossing is a process that brings the genetic material into the same compartment, that is, generating the pre-genetic recombination state).

The mechanisms of outcrossing that are available to a lineage will depend on the characteristics of that lineage as well as their physical proximity to potentially donating organisms. The most familiar of outcrossing processes are found in the various eukaryotic sexual cycles where haploid cells fuse in a process known as fertilization that is followed, either directly or after multiple rounds of mitosis (constituting a pre-genetic recombination state), with meiotic division. Here, by and large, the amount of DNA received is equal to the amount of DNA donated, that is, each parent supplies approximately 50% of the genetic material to the resulting recombinant progeny. A similar sharing of genetic material is seen with coinfecting viruses, i.e., two or more viruses that infect the same cell. Just as with meiosis, the amount of genetic material sourced from any one parent that finds its way into any one progeny will vary from none to 100%, but on average, all else held constant, the fraction of progeny contributed to by any one parent will be equal to the inverse of the number of parents involved in the mating (that is, if five viruses infect a single cell, then on average one-fifth of the genetic material of progeny viruses will have descended from each of the coinfecting parents).

All other forms of outcrossing are not nearly so equitable but instead tend involve the recombination of small amount of genetic material into a larger genome. With viruses, this might be host genetic material or, alternatively, viruses that are associated with the host but which are not concurrently replicating (e.g., proviruses). With bacteria, "snippets" of genetic material may be acquired via at least three different mechanisms including through bacteria-encoded transformation mechanisms (in which naked DNA is taken up from the environment) or through phage-mediated transduction mechanisms.

DNA that otherwise is carried on plasmids also may be made available for recombination with the host chromosome . Indeed, genetic recombination in at least some capacity may be said to occur upon plasmid acquisition by a bacterium, implying that plasmid acquisition is sexual even when it does not involve molecular recombination. Alternatively, one may consider a plasmid-containing bacterium to represent a pre-genetic recombination state on par with karyogamy, endosymbiosis, or post-fertilization but pre-meiosis diploidy.

You are What You Eat

Eukaryotes are able to recombine with virus-carried DNA or pretty much any other DNA that manages to make its way into the nucleus. Indeed, so-called DNA vaccines generate immune responses by forcing eukaryotic cells such as our own to take up either naked or virus-encapsidated DNA, which is then expressed. Gene therapy of eukaryotes similarly can involve not just in expression of virus-transferred DNA but also DNA integration into human chromosomes (by integration I mean some form of illegitimate, micro-homologous, and/or heterologous recombination that results in DNA being inserted into the host chromosome). In short, eukaryotes can be surprisingly promiscuous in terms of the source of DNA that they acquire. Consistent with this possibility, over the course of the evolution of eukaryotes a significant source of acquired DNA seems to have been from bacteria as well as other cellular organism that have served either as food or as endosymbionts to eukaryotic cells.

The latter mechanism may be described as the "you are what you eat" hypothesis (Doolittle, 1998), which is to say that DNA that manages to find its way into the cytoplasms of eukaryotic cells will, with some low but nevertheless finite probability find its way into the nucleus, whereupon integration may occur (the time during which the DNA is present in either cytoplasm or nucleus, but not yet integrated into a cell's chromosome, can be described as representing a pre-genetic recombination state). This can be readily viewed in terms of phagocytosis. There food materials, including, for example, bacteria, viruses, and other eukaryotes, may be internalized into food vacuoles, a.k.a., phagosomes, that are found within the cytoplasm of the phagocytic cell. Normally phagosomes will then fuse with lysosomes, forming phagolysosomes within which the food is digested for subsequent uptake across the phagolysosomal membrane. One can envisage things going wrong with this process, however, such that the barrier separating the phagolysosome lumen from the cytoplasm is breached. In this case, the consuming eukaryotic cell may have foreign DNA contaminating its cytoplasm which, with some low probability, will find its way to the nucleus, whereupon integration may occur.

Many types of organisms can serve as food for phagocytic cells. By contrast, only a few varieties may serve as endosymbionts. The latter are bacteria, as well as a few eukaryotes, that reside and replicate within the larger organism's cytoplasm. Most notably these include the mitochondria found within most eukaryotic cells and the plastids found within the cytoplasms of plants and algae. In this case, genetic exchange, usually from endosymbiont to host cell, occurs when breaches occur in the membranes separating the endosymbiont's cytoplasm from that of its host. Though again with some low but nonetheless finite probability, that DNA can find its way into the host's nucleus whereupon integration can occur.

One additionally can envisage more complex pathways of DNA acquisition that involve combinations of the above-noted pathways. For example, virus DNA, following virion decay, could be taken up by bacteria via transformation. That same DNA could then be moved to a second bacterium by a phage via a transduction process. The second bacterium could then become acquired by a eukaryote as an endosymbiont, and the hosting eukaryote might then be consumed by a phagocytic protist, etc. With each added step the chain of processes becomes much lower in probability. The consequence is that the less closely related entities are to each other the less likely they are to share genetic material, but nonetheless over evolutionary time a great number of genes can move between lineages even despite the existence of what would appear to be substantial barriers to such movement.

Mechanisms of Outcrossing in Bacteria

There are a number of ways by which outcrossing is effected among bacteria. These include transformation, transduction, and conjugation. Interestingly, it can be argued that none of these processes exist as evolved mechanisms of bacterial horizontal gene transfer (Redfield, 2001) . On the other hand, relatively newly recognized mechanisms of bacterial horizontal gene transfer may have a greater likelihood of representing adaptations that exist for the sake of genetic transfer between bacteria, i.e., so-called gene transfer agents as well as vesicle-associated transformation. In this section I discuss these pathways in greater detail in terms of both their mechanisms and potential impact. A review of the molecular underpinnings of transformation and conjugation is available from Chen et al. (2005) .


Transformation is the acquisition, by bacteria, of naked DNA from the environment. An ability to be transformed in the wild does not appear to be universal among bacteria. Those bacteria that are transformable, however, are described as displaying natural competence. Transformation probably is unique among mechanisms of horizontal gene transfer associated with bacteria in that its "range" in many instances is exceeding broadly, at least as a DNA-uptake mechanism. That is, the source of the DNA can have little bearing on the ability of a bacterium to take the DNA up into its cytoplasm. As a consequence of this relative lack of selectivity, transformation can be viewed as a or perhaps even the primary mechanism by which non-bacterial DNA can migrate into the bacterial realm, such as that emanating from domains Eukarya or Archaea, as well as a key mechanism by which bacterial DNA can move between disparate bacterial lineages. The latter claim is perhaps less certain since it is possible that additional mechanisms of DNA acquisition by bacteria, such as transduction and conjugation, could display similar breadth of at least in terms of "serially" overlapping ranges.

Notwithstanding these speculations, the likelihood that transformation-acquired DNA will successfully integrate into a recipient's genome appears to be a function of how well its sequence matches that of already present DNA, at least as has been determined in a Bacillus subtilis system (Roberts and Cohan, 1993) . In addition, apparently the likelihood of recombination between divergent sequences can be increased given mutations in recipient proofreading capacity; see Rayssiguier et al. (1989) as cited by Roberts and Cohan (1993) .


Transduction is the movement of bacterial DNA between bacteria as mediated by phages, or as mediated by other viruses among the organisms found in other domains. In general the potential for a phage to move DNA between bacteria is limited by the phage's host range. Here host range, however, must be defined fairly broadly as an adsorbable host range rather than infectable host range. That is, the ability of phages to move DNA between disparate bacterial lineages is likely greater than traditional measures of host range would indicate. On the other hand, the potential for phages to transport DNA between less-closely related bacterial lineages has been surprisingly poorly explored experimentally (Hyman and Abedon, 2010) .

In comparison with transformation, transduction provides means by which rather large pieces of DNA may be transferred, e.g., 50 kb and more, which can accommodate the movement of even relatively large plasmid DNA. Not all mechanisms of transduction, however, are capable of handling such large pieces of DNA. Nevertheless, presumably the most important mechanism of phage-mediated movement of DNA, at least to bacteria, is so-called generalized transduction (which also can be called "common" transduction), and this is the mechanism which possesses the potential to move these very large pieces of DNA. Alternative mechanisms, such as specialized transduction, or the carriage of morons, are both much more selective in what they move and are able to move only much smaller amounts of bacterial DNA. These other, non-generalized forms of transduction can compensate for these limitations, to a degree, by being able to move DNA in a form that which is potentially amplifiable independent of its acquisition by a bacterium, i.e., in the course of productive phage infections.


Conjugation is an infectious mechanism of plasmid transfer that, unlike generalized transduction, does not involve the destruction of the donating bacterium (i.e., as occurs upon phage-induced bacterial lysis). The transferred plasmid can carry a variety of genes, including what otherwise could be host genes but that have recombined into the plasmid. Most notably, in terms of medical microbiology, conjugative plasmids often carry antibiotic-resistance conferring genes. The plasmid-encoded transfer mechanism also can be co-opted by non-self-transmitting plasmids for infectious movement to new bacteria, with these other plasmids in a sense parasitizing the self-transmissible plasmid-encoded transfer apparatus.

No recombination with the host chromosome is necessary to result in DNA acquisition via conjugation. This is because plasmids replicate in temporal but not physical association with the bacterial chromosome. In some instances, however, plasmids have integrated into the host chromosome, which can result in the transfer of host DNA during the otherwise plasmid-transfer process. It is difficult to say, though, just what might be the significance of this latter process in the wild. Nonetheless, plasmid transfer, whether by conjugation or, presumably more rarely, by transduction, is an important means by which genes, particularly genes that are not always necessary for bacterial prosperity, are shared among bacteria.