The formation of new genotypes by homologous recombination is what is most commonly referred to as sex in bacteria because its outcome more closely parallels that of higher eukaryotes. …bacterial sex can also introduce completely novel sequences to the genome (lateral gene transfer) and augment the gene repertoire of the recipient cell. Such acquisition events can result in fundamental changes in the microorganism's lifestyle; for example, the incorporation of pathogenicity islands… and numerous metabolic pathways and antibiotic resistance genes… — Herma P. Narra and Howard Ochman (2006)

The evolution of individuality was a key step in the evolution of life. It meant that an organism was able to display a more elaborate phenotype without inevitably sharing that phenotype with others. Just as we see in modern human societies, prevention of sharing often means the erection of barriers. This has the effect of keeping one's belongings in place (here, phenotype), including preventing the filching of those belongings by others. Barriers, though, do not just prevent exploitation. They also, perhaps inadvertently, can block beneficial interactions with what thereby becomes the outside world, including cooperative interactions with others as well as the acquisition of various, potentially useful resources that are located on the outside of bodies or cells. Thus, as with most adaptations, though presumably advantageous there nonetheless there exist tradeoffs associated with the evolution of individuality.

With time all of these mechanisms that gave rise to some semblance of individuality were breached. Parasites as well as predators evolved to exploit even seemingly protected phenotype on the one hand while individuals came up with ways to more widely disseminate their phenotype on the other. The latter includes, for example, the export of hydrolytic enzymes towards environmental exploitation, an act that may have been trivial prior to the erection of phenotype-protective barriers but which requires relatively elaborate secretion systems now.

We can envisage that these same phenotype-protecting adaptations may also have had the effect of protecting genotype, that is, an organism's hereditary material. A parallel sequence of evolutionary events thus seems likely to have occurred with regard to gene exchange. Barriers at first likely were few and gene exchange rampant. Then barriers were put in place, presumably to reduce the exploitation of phenotype by others, but to the effect that gene exchange was perhaps dramatically reduced (reductions in access to phenotype by others resulting in reductions in access to genotype). Then, both intentionally and unintentionally, these genetic barriers were reduced and gene exchange, in many lineages, again became at least relatively rampant.

In this chapter I consider both the means and consequences of gene exchange among organisms, a phenomenon more commonly known as sex. The consequences of organism participation in sex include species cohesion, the biological species concept, the breaking up of epistatic interactions along with linkage between coevolved genes, the loss of genotypes that otherwise have stood the test of natural selection (or their failure to form in the first place, i.e., as due to linkage equilibrium), avoidance of Muller's ratchet, increased amounts of genetic and consequently phenotypic variability among individuals, the bringing together of alleles that otherwise would be found in different lineages, more efficient removal of deleterious alleles from populations, avoidance of clonal interference, reduction or elimination of periodic selection, increased rates of adaptation resulting from increased genotypic variation, and, perhaps, disruption of coevolved selfish gene complexes. Different species participate in sex to different degrees, by different mechanisms, and with different benefits or costs depending on other species characteristics (e.g., mutation rates). In this chapter I consider the many routes and consequences of gene exchange involving microorganisms, focusing particularly on horizontal gene exchange, i.e., introgression among bacteria.

Part I:

Part II: (this second part is relatively short, focusing especially on the actual mechanisms of gene exchange, i.e., conjugation, transformation, and transduction as well as "You are what you eat")

Part III: (for technical reasons I had to split the last of the lectures into two, thus III and IV rather than just III; as a consequence, this lecture ends jarringly abruptly… sorry about that…)

Part IV: (as this lecture ends I feel a bit "naked" as the background seems to have been lost in the final, ending interval…)

Vocabulary

Table: Important Terms and Concepts Concerning Gene Exchange.
Term	Definition/Discussion
Biological species concept	Idea that two populations represent different species if individuals from each population are somewhat unable despite opportunity to mate to produce successful hybrid progeny.
	The biological species concept, considered generally, posits that species cohesiveness is a consequence of a relative ease of gene exchange among conspecifics. Thus, here "mating" must be interpreted broadly to mean at least the first steps of gene exchange involving transfer of one organism's genetic material into another, and hybrid progeny should be taken to mean recombinant products of gene exchange. The biological species concept in this way may be applicable to organisms that do not display high rates of genetic exchange but which exchange genes instead via mechanisms that may reasonably be described as mediators of horizontal gene transfer, i.e., conjugation, transformation, and perhaps especially transduction. Horinzontal gene exchange, that is, does not just occur between species but instead can also occur among conspecifics, and indeed may be more prevalent among conspecifics than between species. Furthermore, horizontal exchange may give rise to sufficient recombination within species so as to promote species cohensiveness and, therefore, an applicability of the biological species concept even to organisms that otherwise at least historically have been viewed as clonal.
Conjugation	Plasmid-mediated mechanism of infectious DNA transfer between bacteria.
	Conjugation can be viewed as being similar to reassortment in that it is a form of genetic recombination that does not necessarily involve molecular recombination.Historically it was viewed as the most important of mechanisms of gene exchange among microorganisms, particularly bacteria, plus is closely tied to the evolution as well as transfer of antibiotic-resistance determinants among bacteria. Subsequently, it came to be appreciated that conjugation in many systems likely is eclipsed by transduction as a means of DNA transfer between bacteria, with the latter seemingly more versatile in terms of what DNA is transferred.
Endosymbiosis	Cell living within another cell, typically in a mutualistic relationship.
	The most familiar endosymbionts are mitochondria and plastids. Whatever its form, however, the acquisition by one cell of a second cell, along with that second cell's genes, can be viewed as a form of gene exchange, or at least acquisition by a cell of genes from an exogenous source. It is a means, in fact, by which enormous quantities of DNA can be acquired by another organism in a single event, and a means by which multiple, highly complex biochemical pathways similarly can be acquired at once.
Epistasis	In terms of phenotype, the impact of one genetic locus on another genetic locus.
	The coadaptation of genes or alleles can be viewed as a form of epistasis (or, at least, resulting in a form of epistasis) and it is the breaking apart of coadapted gene complexes that can represent one cost of gene exchange. In particular, specific metabolic pathways can be functionally ineffective if even one of a number of underlying genes is absent. In addition, the gene swapping associated with homologous recombination can result in the replacement of an allele that is more coadapted with one that is less coadapted with other alleles found in the same genome. Epistasis, in other words, turns out to be a very important consideration when considering the costs and benefits of gene exchange, such as in terms of the potential for the product a given gene exchange even to become fixed within a population.
Genetic recombination	Mixing together of the genetic material coming from different sources and employing mechanisms particularly as seen during meiosis.
	Genetic recombination thus consists of some combination of molecular recombination/crossing over along with reassortment/independent assortment. In addition, and more so than necessarily reproduction, genetic recombination is the general endpoint of successful sexual processes (since sex and reproduction are not associated in all organisms but genetic recombination and sex are). Genetic recombination in combination with outcrossing (the acquisition of the to-be-genetically recombined genetic material from a different organism) basically is the definition of sex.
Heterologous recombination	Non-reciprocal gain or loss of genetic material from chromosomes.
	This is more than gain or less of a few nucleotides but instead involves relatively long deletions. Alternatively, and especially as viewed from an evolutionary perspective, heterologous recombination can result in the gain of relatively long segments of genetic material. These gains especially can be viewed as insertions which, in turn, can supply to an organism literally new genes, as opposed to the replacing new alleles with old ones, i.e., heterologous recombination is other than gene swapping. See also the concept of morons as well as that of illegitimate recombination (and also site-specific recombination). Heterologous recombination generally occurs at substantially lower rates than does the majority of homologous recombination evens but also has the potential to much more substantially modify recipient genomes (as well as, presumably in most cases, substantially disrupt those genomes).
Homologous recombination	Means by which the alleles found in otherwise independent chromosomes can be swapped, thereby creating especially subtlety novel combinations of alleles within a single organism.
	Also described as crossing over or (especially here) molecular recombination, homologous recombination requires relatively substantial sequence similarity before allele exchange can commence (i.e., high degrees of sequence homology). In many though not all instances homologous recombination is not heterologous but instead involves a swapping of genetic material between chromosomes.
Horizontal gene transfer	Movement of alleles between individual organisms but other than from parent to offspring.
	This is particularly movement of alleles between organisms other than in the course of sexual reproduction. Equivalently, see lateral gene transfer or horizontal gene exchange versus vertical gene transfer or vertical inheritance. Typically horizontal gene exchange is abbreviated as HGT. In bacteria the primary mechanisms by which the gene transfer of horizontal gene exchange is effected is via conjugation, transformation, and transduction. Also as applied to bacteria, see also the concepts of introgression as well as genetic migration.
Illegitimate recombination	Gene exchange between two molecules of nucleic acid that occurs by poorly defined mechanisms and which involves little or no identity prior to crossing over.
	Illegitimate recombination is a grab bag term that describes what typically are assumed to be either errors in normal mechanism of homologous recombination or which occur instead outside of these otherwise normal mechanisms of molecular recombination. In any case, illegitimate recombination is a form of molecular recombination rather than a form of either independent assortment or reassortment. Illegitimate recombination can potentially give rise to highly novel gains in genetic material in association with resulting heterologous recombination events. Illegitimate recombination and heterologous recombination, however, are not identical phenomenon with illegitate recombination referring to the means by which molecular recombination is initiated and heterologous recombination referring instead to one possible consequence of molecular recombination.
Introgression	Low-level gene flow between species.
	Traditionally the term introgression has been used to describe the exchange of genes between what otherwise are reasonably well defined biological species and as occuring via normal sexual reproduction mechanisms. The resulting introgression nonetheless is at least somewhat similar to the horizontal gene transfer such as can occur between bacteria as a consequence of especially transformation or transduction. Here this more general sense of introgression – low-level gene flow in the course of either horizontal gene transfer or instead vertical inheritance – is implied. Note that introgression can occur as a consequence of either homologous recombination or illegitimate recombination and can result in either gene swapping or instead in some form of heterologous recombination, particularly the gain by a genome of additional as well as somewhat novel genetic material.
Lateral gene transfer	Allele movement between individuals that occurs other than in the course of sexual reproduction.
	Lateral gene transfer thus is essentially the equivalent of horizontal gene transfer and contrasts with the vertical movement of genetic material directly from parent to offspring.
Linkage	Close physical proximity especially of loci on chromosomes.
	Linkage more broadly describes a difficulty in separating alleles from each other, whether found on the same chromosome or instead located within the same cell if that cell does not participate in gene exchange with other cells. One can define this broader perspective on linkage in terms of alleles displaying what can be described as co-transmission or co-inheritance. Linkage additionally and indeed equivalently gives rise to linkage disequilibrium, which is a statistical description of such co-transmission or co-inhertiance certainl alleles with each other but not with other, otherwise equivalent alleles.
Linkage disequilibrium	Failures of alleles to be separated by recombinaion across a population and otherwise in the course of their inheritance.
	Linkage disequilibrium is what occurs when either recombination fails to adequately separate alleles or instead because such separation is selected against. Classically this occurs particularly when the extent sexual processes, particularly sexual reproduction within populations, is inadequate to support the unlinking of closely located, i.e., linked alleles. Linkage disequilibrium nonetheless can describe any situation where separation of alleles should be at least possible but nonetheless greater than statistically expected levels of association remain. The "equilibrium" of linkage disequilibrium refers to random distribution of alleles across individuals making up populations, that is, what one would expect given effectively infinite amounts of gene exchange among organisms and associated shuffling of genomes in the course of homolous recombination. Mostly clonal populations such as those of many bacteria can display substantial levels of linkage disequilibrium, and one of the consequence of horizontal gene exchange-like mechanisms can be a reduction in linkage disequilibrium.
Lysogenic conversion	Modification of the phenotype of host bacteria through gene expression by prophages.
	Prophages are symbiotic associations between bacteriophage genomes and bacteria. In moving between bacteria, temperate bacteria carry their genes, thus giving rise to a form of gene exchange or transfer that can be viewed as a kind of specialized transduction. These phages can carry numerous genes, many of which may be of bacterial origin, and which otherwise may be helpful upon expression within bacteria. Many of these prophage-expressed genes encode bacterial exotoxins and virulence factors. In terms of phage evolution, it is important to consider how these genese may contribute to phage fitness, particularly as viewed within the context of the phage ecology of either lysogenic cycles or instead especially induced lytic cycles. See also the concept of morons.
Migration (genetic)	Movement of alleles into or out of populations.
	As this is gene exchange between populations, to a degree it can be viewed basically as synonymous with horizontal gene transfer, which also may be described as introgression. That is, if gene exchange is too frequent between two populations then the status of those populations as separate or distinct can be questioned, so genetic migration inherently must occur beteween two distinct polations at a moderately low rate. Alternatively, if populations are defined in terms of the extent to which gene exchange occurs within them, then for organisms that are highly clonal essentially all gene exchange can be decribed in terms of genetic migration, horizontal gene transfer, or introgression.
Molecular recombination	Exchange, replacement, or insertion of sequences especially between, of, or into DNA molecules.
	Molecular recombination is more or less equivalent to crossing over. I use this term to provide a general contrast to reassortment. That is, genetic recombination consists of reassortment (or independent assortment) and/or molecular recombination (or crossing over). Note that in the definition the implied phrases ae "Exchange between", "Replacement of", and "Insertion into" DNA molecules.
Moron	Genes acquired particularly by bacteriophages and especially via illegitimate and/or heterologous recombination.
	Moron essentially stands for "More DNA", which is in addition especially to those genes required by a phage for productive infection. Moron can be involved instead in lysogenic conversion, though not all converting genes are morons nor all morons necessarily expressed during lysogenic cycles. The acquisition of a more can be viewed as a random event, in many ways equivalent to mutation though in which genetic material that has likely already been subject to the text of natural selection has been acquired. Whether that genetic material is retained within a population, however, is dependent on whether its acquisition is disruptive to the receiving organism, whether it supplies a benefit to the receiving organism, and to what degree the receiving organisms otherwise is able to integrate the genetic material and its expression into its physiology.
Muller's ratchet	Manifestation of genetic drift where, in small, non-sexual populations, there will be a tendency from the wild-type genotype to be lost.
	Here Muller's ratchet is highlighted not as a consequence of gene exchange but instead as a possible consequence of an absence of gene exchange. One benefit of gene exchange between organisms thus can be an interference in the ability of Muller’s ratchet to occur within a population, though note that this is only true to the extent that the gene exchange involved has some reasonable potential of restoring otherwise lost wild-type genotypes.
Outcrossing	Movement of genetic material between different organisms.
	Outcrossing contrasts especially with forms of meiosis-based reproduction that does not involve the fusion of gametes that have been sourced from different parents. Nonetheless, outcrossing serves as good descriptor for all manner of sexual processes in which the genetic material sourced from two different organisms finds its way into the same cell. This can be in the course of sexual reproduction (as in the course of and then following mating) or instead in the course of horizontal gene transfer. Sexual process thus generally though not quite always involve outcrossing and this is along with genetic recombination.
Periodic selection	Deterministic increases in the representation of certain genotypes within clonal populations.
	Here periodic selection is highlighted not as a consequence of gene exchange but instead as a possible consequence of an absence of gene exchange. In particular, without gene exchange then natural selection acts especially on genotypes whereas with gene exchange it instead is individual alleles or instead complexes of individual alleles that natural selection does or does not bias the propagation of. Another way of stating the same thing is that periodic selection is one consequence of high levels of genetic linkage among alleles, that is, high levels of linkage disequilibrium.
Reassortment	Genetic recombination that does not involve molecular recombination and as is seen particularly with gene exchange among certain viruses.
	Reassortment is somewhat equivalent to independent assortment as a mechanism of genetic recombination, where independent assortment is ssen particularly during meiosis while reassortment is seen during non-meiotic sexual pocesses. Reassortment is seen with viruses that display what are known multipartite genomes, that is, which consist of multiple, non-homologous segments. The most recognizable multipartite virus is influenza virus and reassortment plays important roles in influenza evolution such as in terms of influenza host range and virulence.
Sex	Movement of genetic material from the cytoplasm, nucleus, or virion of one individual to that of another, where stable incorporation of that genetic material in the recipient can be viewed as a successful endpoint.
	Sex comes in numerous forms ranging from that associated with sexual reproduction to that associated instead with horizontal gene transfer, that is, which is not directly associated with reproduction. Sex similarly does not necessarily involve relatively equal contributions by two parents to the genetic complemenet of resulting recombinant progeny. Horizontal gene transfer in general, as a sexual process, in fact involves the acquisition by one individual of only relatively small segments of genetic material.
Transduction	Accidental, virus-mediated movement of non-virus DNA between cells.
	Transduction can involve both functional and otherwise non-functional virus particles. The latter especially, in the guise of what is known as generalized transduction, can carry large segments of DNA between organisms such as bacteria, e.g., up to tens of thousands of nucleotides or more. See also the concepts of morons and lysogenic conversion.
Transformation (genetic)	Uptake of naked DNA by a cell, potentially resulting in recombination into the cell's genome.
	Not all organisms are adept at picking up naked DNA from their environment, though those that can are referred to as naturally competent. Transformation can result in gene exchange betwee substantially different organisms but typically this involves the acquisition of relatively short segments, e.g., as compared with what is possible instead with transduction.
You are what you eat	Acquisition especially by phagotrophic eukaryotic cells of DNA associated with prey organisms that they have engulfed.
	The basic idea behind 'You are what you eat' is that it is possible for genetic material to 'escape' from intracellular compartments (especially phagosomes, a.k.a., food vacuoles) into a eukaryote cell's cytoplasm. From there movement is possible into the nucleus along with subsequent heterologous and/or illegitimate recombination. Sexual exchange to phagotrophic and particularly single-celled eukaryotes thus can in principle be highly promiscuous. The processes involved in 'You are what you eat' mechanisms also are similar to those involved in the nuclear acquisition of genes from endosymionts such as mitochondria and plastids.