Mutation

Hi again! Where does diversity come from? How did we get so much variation out there in nature (and also even within ourselves o.O)?

Today's subject: mutation!

Even though mutations often have a negative connotation, they are the main - and arguably only - constructive evolutionary force. Mutations are what give all the other forces something to work with: variability.

So, what are exactly mutations? I suppose most people have some understanding of what they are, considering how common words like "mutant" and "mutation" are in the pop culture (e.g. Teenage Mutant Ninja Turtles, X-Men, Hulk, Bioshock, etc.). Well, mutations are very simple. They are nothing more than changes to the genome of any living being (including even viroses!).

There are many ways in which mutations can happen, but these events can be categorised in simple manner in two groups: substitutions and indels (insertion/deletion). As you may know, DNA is formed by a sequence of nucleotides (A, C, G or T). Whenever one nucleotide is replaced by one other nucleotide (e.g. ACACAA --> ACATAA), this is called a substitution (or point mutation). When one letter disappears (e.g. ACACAA --> ACA-AA), it is a deletion; when a letter is added (e.g.  ACA-AA --> ACACAA), that is an insertion. These indels are structural changes and they can happen at large scale: Making copies of big chunks of a chromosome (duplications), Inverting the same big chunk and putting it back (inversions), or simply deleting a big chunk (also called deletions). Also, if two big chunks of DNA swap places, that is called a translocation.

Mutations can also be classified based on the effect they have on the fitness of the individual carrying it. They can be deleterious, nearly-neutral, neutral or beneficial, with negative to positive effect in the order they are listed. Mutations can yet be classified according to the effect on protein sequence (when they happen on protein-coding DNA), which kind of cell they occur in, or even their effect on function (which overlaps a lot with fitness effect).

Something that is particularly interesting about mutations is that, on the long term, they tend to happen with a predictable frequency - e.g. one mutation per nucleotide every million years. This may sound like a very rare event, but bear in mind that, even though this varies a lot in different organisms, genomes tend to have billions of nucleotides! This means that, in a genome of 1 billion nucleotides (or base pairs, bp for short), 1 thousand mutations will occur every year, in average. This property of mutations has been widely used to figure out when evolutionary events happened. If you compare the genomes of two species and observe that they are different in say 2% of their nucleotides, and if you an approximate divergence rate (e.g. 1% per million years), you can assert that these two species are separated for approximately 2 million years (plus or minus a confidence interval).

All in all, evolution would not happen without mutations! They are a necessary evil, one could say. But there is more to them. In the near future, we'll have a look on the effect of mutations in small populations. Spoiler alert: it's not good...

See you next time. Cheers!

Drift, Genetic Drift

It was difficult to chose which would be the first post on this blog. There are so many different subjects that could be just as nice, but here goes. Today, we'll speak about genetic drift and, with it, start the series Evolutionary Forces.

So, first off, what are evolutionary forces? In a nutshell: forces that drive evolution. Biological evolution, that is. Well, what is biological evolution then? (We will call it just evolution anyway, OK?) Evolution is nothing more than change over time. Therefore evolution is not - as some people say - just a theory. It simply is the observed fact in the world that things tend to change, more and more, as time goes on. This applies to stars, planets, continents, rocks, and living things, being part of the universe, are no exception.

The mechanisms through which these changes happen in living beings, as well as the patterns left by them, is the subject of study for evolutionary biologists. Since the modern synthesis, four evolutionary forces have been recognised: (i) genetic drift, (ii) mutation, (iii) migration, (iv) natural selection. These can be analysed according to their effect on diversity. While mutation and migration create diversity (constructive), drift and selection are destructive forces, eliminating diversity either systematically or randomly.

Genetic drift is a random destructive evolutionary force. This means that drift leads to the loss of diversity in a random way. Let's analyse these two properties separately. Drift is a random process because any given allele (a genetic variant) in the population has the same chance of success in reproduction and survival. It is simply a lottery: whichever allele is lucky enough to be drawn will remain in the population.

In the figure bellow (from Wikipedia), we have an example. In the first jar we see a population with 50% red and 50% blue marbles. Now, imagine you (yes, you!) want to do a lottery draw to see what will be the next generation's composition. Now, there is important thing to observe: We can only fit 20 marbles inside a jar. What you do is to put your hand inside jar #1 and take one marble without looking (don't peek!)

OK, now put it back! And you may say: "Wait! Why?". Then I will say: "Very good question!". Well, here is why: what we are sampling are in fact genes that are passed to the next generation, not individuals. So, by chance, one lucky marble may have two kids while the other had none. That's what we're doing by putting the marble back in the "gene pool". For it to have a chance of being present two, three or more times in the following generation. So, what you do in reality is to take note of whatever marble color (allele) you took and put it back. When you're done with 20 drawings (the total amount of marbles we can fit in the jar), you go to your big stock of marbles (because you have a lot of them) and take enough marbles to fill the next generation's jar with the lucky alleles you have in your notes.

Now, if you repeat this process some times, you will always end up with one or the other allele (blue OR red) being the only kind you have in the entire population. And when you have only one kind of something you have zero diversity. Therefore a destructive process! If we had only drift happening in nature, there would be no diversity, and to be clear nearly no evolution.

There is one more detail, though. If you try to repeat this little experiment with much bigger jars with room for say 200 individuals, it will in average take you much longer to reach o monomorphic state (only red, or only blue). Actually, even our little example was quicker than the expected average. In a population of 20 marbles, the average time to have only one kind of marble is 40 generations. In a population with 200 marbles, this will take 400 generations! In a very very large population of 1 million marbles, it will take 2 million generations. Well, I guess you got it, right? It takes in average twice as much generations as you have of marbles (or chromosomes!) to reach a state with zero diversity.

If we want to make this whole story become more realistic (because we see diversity out there in nature!), at least one more thing is missing. We need new things to appear in the population. In the next article in the series, we'll look at mutation and how it brings diversity to populations. However in the next post - before looking at mutation - we'll see that alleles can surf! We'll investigate the intriguing phenomenon of allele surfing and see how this surfing is deeply related to genetic drift.

See you then!