Basic Concepts: Allele

One of the perennial favorite targets of anti-evolutionists is the field of molecular systematics. Molecular systematics, for those of you who are not familiar with the term, refers to the practice of using biological molecules - things like proteins, DNA, and RNA - to study the evolutionary history of groups of organisms. Molecular systematics is yet another one of those areas of evolutionary biology that is easy to misrepresent, and hard to understand. I'm going to (slowly) try to get posts up explaining the field in basic terms, starting with the basic vocabulary. This post is the first of the series, and will cover one of the most basic terms used in both molecular systematics and population genetics: allele.

A simple definition of allele can be found in textbooks such as "Biology, Sixth Edition" (Neil A. Campbell, Jane B. Reece):

Alleles: Alternate versions of a gene.

If we are going to talk about alleles in the context of molecular systematics, there are a couple of areas in that definition that need clarification. The first involves the definition of "gene," while the second involves the different types of molecular markers that can be used in molecular studies. We'll take them one at a time.

If you've been following the Basic Concepts series of posts here at Scienceblogs, you already know that we've already seen several different definitions of "gene." The definitions differ in small, but significant ways, so it's probably a good idea for me to specify which one we're using when we define "allele." In this particular case, we are using any and/or all of those, plus a few more that aren't there. As long as the definition of gene includes something about a gene being inheritable, it will work fine for defining allele. Since the definition of "allele" will work for any (reasonable) definition of gene, there's no need to change the simple definition to specify any particular definition.

The second issue - the different types of molecular markers - does require a bit more clarification. There are a number of different techniques that can be used to detect genetic differences. These techniques are not equally sensitive, and will not detect the same number of alleles for a particular gene.

For example, genetic diversity can be measured using proteins as markers for genes. Some of the methods for doing this will only detect differences if the alternate forms of the protein have different electrical charges. This means that variants of the protein that have the same (or very similar) charges will not be identified as being different.

At the other extreme, there are DNA-based methods of measuring genetic diversity that look at the number of times a particular small sequence is repeated within a particular gene. These changes may not do anything at all to the gene or to how it is regulated, and may not do anything at all to the organism - which means that they are irrelevant as far as natural selection is concerned.

There are reasons for using different types of markers, but those reasons are complex enough that I'll delay talking about them until another post. The important point for now is simply that the genetic diversity detected using one kind of marker can't easily be compared to the genetic diversity detected using another type of marker. That point is important enough that it's probably worth adding a few words to the simple definition to make sure that it is clear.

Alleles: Alternate versions of a gene that are detectable using a particular set of techniques.

In future posts, this is the definition that I'll be using when I talk about molecular systematics and population genetics.