So far, we have not worried overly much about the organization of genes in an organism. It could be that each gene behaves like an isolated object, but in fact that is not the case. We bring it up here because the way genes are organized can, in fact, influence evolutionary processes. In his original genetic analyses, Gregor Mendel (1822–1884) spent a fair amount of time looking for “well behaved” genes and alleles, those that displayed simple recessive and dominant behaviors and that acted as if they were completely independent from one another. But it quickly became clear that these behaviors are not how most genes behave. In fact, genes act as if they are linked together, because they are (as we will see, gene linkage arises from the organization of genes within the DNA molecules.) So what happens when a particular allele of a particular gene is highly selected for or against, based on its effects on reproductive success? That allele, together with whatever alleles are found in genes located near it, are also selected. We can think of this as a by stander (or sometimes termed a “piggy-back”) effect, where alleles are being selected not because of their inherent effects on reproductive success, but their location within the genome.
Linkage between genes is not a permanent situation. As we will see toward the end of the course, there are processes that can shuffle the alleles (versions of genes) on chromosomes, the end result of which is that the further away two genes are from one another on a chromosome, the more likely alleles of those genes will appear to be unlinked. Over a certain distance, they will always appear unlinked. This means that effects of linkage will eventually be lost, but not necessarily before particular alleles are fixed. For example, extremely strong selection for a particular allele of gene A can lead to the fixation of mildly deleterious alleles, in neighboring regions. We refer to a position of a particular gene within the genome as a genetic locus (or the plural, loci). In Latin locus means ‘place’ (think location, which is derived from the same root). A particular genetic locus can be occupied by any of a number of distinct alleles (DNA sequences). As we will see, there are various mechanisms that can duplicate, delete, or move within the genome a region of DNA, creating (or eliminating) new genetic loci. The phenotype associated with an allele is influence by its genetic locus, as well as the details of the rest of the genome.
It is worth noting the combination of non-adaptive, non-selective processes can lead to the appearance and maintenance of mildly non-advantageous traits within a population. Similarly, a trait that increases reproductive success, by increasing the number of surviving offspring, may be associated with other not-so- beneficial, and sometime seriously detrimental (to individuals) effects. The key is to remember that evolutionary mechanisms do not necessarily result in what is best for an individual organism but what in the end enhances net reproductive success. Evolutionary processes do not select for particular genes (we will consider how new genes appear later on) or new versions of genes but rather for those combinations of genes that optimize reproductive success. In this light, talking about selfish genes, as if a gene can exist outside of an organism, makes little sense.
Of course, the situation gets more complex when evolutionary mechanisms generate organisms, like humans, who feel and can actively object to the outcomes of evolutionary processes. From the point of view of self-conscious organisms, evolution can appear cruel. This was one reason that Darwin preferred impersonal (naturalistic) mechanisms over the idea of a God responsible for what can appear to be gratuitously cruel aspects of creation.