In the last post in this series, we examined how DNA variation arises as chance events, such as base-pair mismatches, duplications and deletions. In order to understand how this variation may (eventually) contribute to a speciation event, we need to discuss how variation spreads within a population. First, we need a small amount of vocabulary to facilitate the discussion: specifically, we need to explain the distinction between a gene and an allele.
As a geneticist, I pull my hair out at times when reading popular media reports of scientific matters. One of my biggest pet peeves is the use of the word “gene” in the sense of saying that an individual “has the gene” for a specific trait. We have already described genes are a section of DNA sequence on a chromosome that contributes to a function of some kind, usually by coding for a protein product. In this sense, humans all have the same genes (or very nearly so)—the 20,000 or so sequences that make us who we are biologically. What we don’t have, however, are identical genes—there are differences that arise through the copying errors that we have discussed. These differences are called alleles. You can think of an allele as a “version” or “flavor” of a gene. Mutation events don’t usually create new genes (though they can through duplication). Usually, new alleles are created. In a prior post, we used children’s toy bricks to illustrate how a new variant could arise through a DNA base-pairing mistake during chromosome replication:
In this example, we have a sequence that, through a copying error, becomes two slightly different versions of what is (almost) the same sequence. These differences would be called two distinct alleles, and if they affect the function of a gene, they might have a noticeable effect at the level of the whole organism. When the media talks about the “gene” for this or that trait, what they actually mean is the allele for a given trait—the specific variant of a gene that is correlated with a specific medical condition, for example.
Selection and drift
So, DNA variation is all about the production of new alleles—but what happens to these alleles over time within a population? Obviously, when a new allele arises, it is present in only one individual. If it is to make an impact on the population as a whole, it needs to spread to other individuals by being passed on to offspring. In this way, variation can enter a population and then become more common over time. There are a number of factors that can influence this process. If the population size is small, then chance alone can increase (or decrease) the frequency of an allele in a population—an effect known as genetic drift. Since drift can be a major player in how allele frequencies change over time in a population, it’s worth taking some time to discuss it in some detail.
Drift is essentially a non-representative sampling event. Consider a small population of sexually reproducing organisms that we can represent as rectangles, each containing two alleles (the squares, with the colors representing allele differences). We can represent their “reproduction” as a 50:50 chance of passing on either allele to their offspring in the next generation. (Note: each “passing” event is independent of any other—for example, there is no mechanism to guarantee that any individual would pass down both of their alleles if they reproduced twice.) For the breeding pair on the left, one parent has two yellow alleles, and the other has a blue allele and a yellow allele. When they reproduce, by chance the parent with both alleles passes on only the yellow allele to both offspring. For the breeding pair on the left, the parent with both alleles also passes on the yellow allele twice, and their blue allele not at all. These chance events shift the frequency of the two alleles quite significantly within one generation:
Now imagine that the offspring pair up to mate, and that once again we have, by chance, a slightly non-representative sampling to form the next generation:
The point is that this small population is prone to large fluctuations in the frequencies of the blue or yellow alleles because it is so small. This small size means that chance events within even one breeding pair have a large impact on the population as a whole. In the next generation, for example, the blue allele might be lost completely—and once it has disappeared, it will be absent until it either arises again through a new mutation event, or enters the population through an individual migrating in from a population where it is still present.
For large populations, however, the situation is rather different. Imagine a population with 1000 individuals, with a total of 500 yellow alleles and 500 blue alleles randomly distributed among the individuals. When this population reproduces, it will never vary much from this 50:50 ratio from one generation to the next. In this large population, chance events within one breeding pair are a very small proportion of the population as a whole, and on average, the population will reflect the 50:50 probability of any allele being passed on.
So, how can allele frequencies change in large populations, when drift is largely impotent? We have already seen one mechanism that can accomplish this: natural selection. Natural selection is simply the effect that individuals who possess a certain allele reproduce more frequently than individuals who do not have that allele. Over time, this skewing of the probability of reproducing increases the frequency of the selected allele in the population. For dogs early in the domestication process, duplication of amylase genes happened as a one-time, chance mutation event. Dogs that carried the duplicated amylase allele reproduced at a slightly greater frequency than dogs without it, since the duplication allele allowed for dogs to derive more nutrition from the food they were receiving from their new environment (i.e. human sources). Over time, the duplicated allele became so frequent in the dog population that the ancestral, non-duplicated allele was lost all together. At this point the new allele was “fixed” in the population: it had a frequency of 100%.
To sum up: in small populations, drift can have a large impact on allele frequencies from one generation to the next. In large populations, natural selection predominates, and drift has little impact. Both of these mechanisms can contribute to changing allele frequencies over time within populations, and as such both can be factors that contribute to speciation events.
Changing allele frequencies and speciation
Speciation is the production of two species from a common ancestral population. (Now, we have already discussed how defining “species” is a fuzzy concept, and it is the fact that they arise slowly and incrementally that makes them challenging to define.)
One way to understand how speciation starts is to consider two populations of the same species, that for whatever reason, stop interbreeding with each other—perhaps through geographic isolation. While a geographic “barrier” has nothing at all to do with genetic differences or reproductive compatibility, if such a barrier is in place, then alleles that arise in one population will not be transferred to the other population. Additionally, if two populations are not exchanging alleles, then allele frequencies in the two populations are now no longer tied to the other and averaged between them. This means that drift and selection will now act independently on the two populations. Once uncoupled, the two populations may then follow different trajectories—one population may start out small, and be dominated by drift until it increases in size. The other population may remain large, and be subject to natural selection in ways the other population is not. Over a long period of time, the two populations may become genetically different enough that they form two distinct species. The key, of course, is the nature of the barrier preventing exchange of alleles between populations. In the next post in this series, we’ll examine how such barriers can form between populations.