In organic life, there are a wide variety of mechanisms by which offspring are produced which contain genetic material from more that one parent. This is the sexual process. Recombination mechanisms range from very primitive and haphazard to elaborately orchestrated.
At the primitive extreme we find certain species of bacteria, in which upon death, the cell membrane breaks open, releasing the DNA into the surrounding medium. Fragments of this dead DNA are absorbed across the membranes of other bacteria of the same species, and incorporated into their genome [59]. This is a one way transferral of genetic material, rather than a reciprocal exchange.
At the complex extreme we find the conventional sexual system of most of the higher animals, in which each individual contains two copies of the entire genome. At reproduction, each of two parents contributes one complete copy of the genome (half of their genetic material) to the offspring. This means that each offspring receives one half of its genetic material from each of two parents, and each parent contributes one half of its genetic material to each offspring. Very elaborate behavioral and molecular mechanisms are required to orchestrate this joint contribution of genetic material to the offspring.
The preponderance of sex remains an enigma to evolutionary theory [5,26,31,32,55,61,86,96]. Careful analysis has failed to show any benefits from sex, at the level of the individual organism, that outweigh the high costs (e.g., passing on only half of the genome). The only obvious benefit of sex is that it provides diversity among the offspring, allowing the species to adapt more readily to a changing environment. However, quantitative analysis has shown that in order for sex to be favored by selection at the individual level, it is not enough for the environment to change unpredictably, the environment must actually change capriciously [13,57]. That is, whatever genotype has the highest fitness this generation, must have the lowest fitness the next generation, or at least a trend in this direction, a negative heritability of fitness.
One theory to explain the perpetuation of sex (based on the Red Queen hypothesis, see below) states that the environment is in fact capricious, due to the importance of biotic factors in determining selective forces. That is, sex is favored because it is necessary to maintain adaptation in the face of evolving species in the environment (e.g., predators/parasites, prey/hosts, competitors) who themselves are sexual, and can undergo rapid evolutionary change. Predators and parasites will tend to evolve so as to favor attacking whatever genotype of their prey/host is the most common. The genotype that is most successful at present is targeted for future attack. This dynamic makes the environment capricious in the sense discussed above.
There are fundamental differences in the nature of the evolutionary process between asexual and sexual organisms. The evolving entity in an asexual species is a branching lineage of genetic individuals which retain their genetic identity through the generations. In a sexual species, the evolving entity is a collective ``gene pool'', and genetic individuals are absolutely ephemeral, lasting only one generation.
Recalling the discussion of ``genotype space'' above in the section ``Evolution in Sequence Space'', imagine that we could represent genotype space in two dimensions, and that we allow a third dimension to represent time. Visualize now, an evolving asexual organism. Starting with a single individual, it would occupy a single point in the genotype space at time zero. When it reproduces, if there is no mutation, its offspring would occupy the same point in genotype space, at a later time. Thus the lineage of the asexual organism would appear as a line moving forward in time. If mutations occur, they cause the offspring to occupy new locations in genotype space, forming branches in the lineage.
Through time, the evolving asexual lineage would form a tree like structure in the genotype space--time coordinates. However, every individual branch of the tree will evolve independently of all the others. While there may be ecological interactions between genetically different individuals, there is no exchange of genetic material between them. From a genetic point of view, each branch of the tree is on its own; it must adapt, or fail to adapt based on its own genetic resources.
In order to visualize an evolving sexual population we must start with a population of individuals, each of which will be genetically unique. Thus they will appear as a scatter of points in the genotype space plane at time zero. In the next generation, all of the original genotypes will be dead, however, a completely new set of genotypes will have been formed from new combinations of pieces of the genomes from the previous generation. No individual genotypes will survive from one generation to the next, thus over time, the evolving sexual population appears as a diffuse cloud of disconnected points, with no lines formed from persistent genotypes.
The most important distinction between the evolving asexual and sexual populations is that the asexual individuals are genetically isolated and must adapt or not based on the limited genetic resources of the individual, while sexual organisms by comparison draw on the genetic resources of the entire population, due to the flow of genes resulting from sexual matings. The entity that evolves in an asexual population is an isolated but branching lineage of genetic individuals. In a sexual population, the individual is ephemeral, and the entity that evolves is a ``gene pool''.
Due to the genetic cohesion of a sexual population and the ephemeral nature of its individuals, the evolving sexual entity exists at a higher level of organization than the individual organism. The evolving entity, a gene pool, is supra-organismal. It samples the environment through many individuals simultaneously, and pools their genetic resources in finding adaptive genetic combinations.
The definition of the biological species is based on a concept of sexual reproduction: a group of individuals capable of interbreeding freely under natural conditions. Species concepts simply do not apply well to asexual species. In order for synthetic life to be useful for the study of the properties of species and the speciation process, it must include an organized sexual process, such that the evolving entity is a gene pool.