3.16: Gene linkage- one more complication

So far, we have not worried much about the organization of genes in an organism. We also have not considered what, exactly a gene is. For now, let us just say that a gene is information encoded within a region of a DNA molecule and that multiple genes are present in a single DNA molecule – we consider genes in detail later (Chapter 7). As you might conclude from genetic background effects, genes and the products they encode interact. We bring this up because the way genes are organized can influence evolutionary processes. As mentioned above, in his studies, Gregor Mendel spent a fair amount of time looking for “well behaved” genes and alleles, those that display simple recessive and dominant behaviors and that act as if they were independent of one another.^[146] As noted by Kampourakis, "Weldon’s (1902) studies of varieties of pea hybrids led him to conclude that there was a continuum of colors from greenish yellow to yellowish green, as well as a continuum of shapes from smooth to wrinkled. It thus appeared that in obtaining purebred plants for his experiments, Mendel had actually eliminated all natural variation in peas, and that characteristics were not as discontinuous as he had assumed". The situation complex for most traits and the genes that influence them. Traits are rarely dichotomous (one or the other), and often influenced by multiple genes. Genes often act as if they are linked together because they often are. Gene linkage arises from the organization of genes within chromosomes; each chromosome is in individual DNA molecules. So what happens to linked genes when a particular allele of a particular gene is strongly selected for or against? That allele, together with the alleles of linked genes, are also "selected". We can think of this as a "by-stander" effect. Their frequency in a population increases or decreases not because of their direct effects on reproductive success, but because of their location within the genome, their “linkage” to an allele that strongly influences selection.

In sexually reproducing organisms the linkage between alleles (genes) is not permanent. There are processes (meiotic recombination) that can shuffle the alleles on a chromosome. The end result of such recombination events is that the further away two genes are from one another on a DNA molecule in a chromosome, the more likely it is that alleles of those genes will become unlinked, that is, have independent effects on reproductive success. Over time, the effects of linkage will be lost, but not necessarily before particular alleles have been fixed and other alleles lost within the population. For example, extremely strong selection for a particular allele of one gene can lead to the fixation of mildly deleterious alleles in closely linked, neighboring genes.

Let us clarify some terms related to genes. These terms arise from the history of biology in general, and genetics in particular. We now know that genetic information is stored in the sequence of double-stranded DNA molecules. A gene is the region of a DNA molecule that encodes a particular “gene product”, either an RNA molecule or a polypeptide, together with regions required for controlling when and where the gene's "product" is “expressed”. Where and when a gene is expressed is regulated by networks of interacting molecules. All of the DNA molecules present in a cell are known collectively as the cell’s genome. We refer to the position of a particular gene within the genome as its genetic locus. In Latin locus means ‘place’; think location – a word derived from the same root. A particular genetic locus can be occupied by any of a number of distinct alleles (DNA sequences). There are various mechanisms in cells that can duplicate, delete, insert, or move a region of DNA within the genome, creating or eliminating new genetic loci. The phenotype associated with an allele can be influenced by its position within the genome.

A trait that increases reproductive success, by increasing the number of surviving offspring, may be associated with other not-so-beneficial, and sometime detrimental (to individuals) effects. The key is to remember that evolutionary mechanisms do not necessarily result in what is best for an individual but what in the end enhances the net (short term) reproductive success of a population. Evolutionary processes do not select for particular genes or new versions of genes but rather for those combinations of alleles that optimize reproductive success. The situation gets more complicated when evolutionary mechanisms generate organisms, like humans, who think and feel and can actively object to the outcomes of evolutionary processes. From the point of view of self-conscious organisms, evolution can appear harsh, or at the very least totally uninterested in the desires and happiness of individuals. This was one reason that Darwin preferred impersonal (naturalistic) mechanisms over the idea of a God responsible for what can appear to be the gratuitously cruel aspects of its creation.

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