There in the foaming welter of email constantly flooding my in-box was an actual, real, good, sincere question from someone who didn't understand how chromosome numbers could change over time — and he also asked with enough detail that I could actually see where his thinking was going awry. This is great! How could I not take time to answer?

So here's the question:

How did life evolve from one (I suspect) chromosome to... 64 in horses, or whatever organism you want to pick. How is it possible for a sexually reproducing population of organisms to change chromosome numbers over time? Firstly: there would have to be some benefit to the replication probability of the organisms which carry the chromosomes. I don't see how this would work. How is having more chromosomes of any extra benefit to an organism's replicative success? Yes, perhaps if those chromosomes were full of useful information... but the chances of that happening are non existent and fly in the face of 'small adaptations over time'. Secondly, the extra chromosomes need to come from somewhere. I'm not sure about this, but I believe chromosome number are not determined by genes, are they? There isn't a set of genes which determines the number of chromosomes an organism has. So the number is fixed, determined by the sexually reproducing parents. Which leads me to believe that if the number does change, and by chance the organism is still alive and capable of sexual reproduction, that the number will start swinging back and forward, by 1 or 2, every generation, and never stabilising. The chances of this happening are also very very slim.

Let's clear up a few irrelevant misconceptions first. Life probably started with no chromosomes — early replicators would have been grab bags of metabolites, proteins, and RNA that would have simply sloppily split in two, with no real sorting. DNA and chromosomes evolved as accounting and archiving tools: they were a way to guarantee that each daughter cell in a division reliably received a copy of every gene. Also, most living things now just have one 'chromosome', a loop of DNA, and perhaps a small cloud of DNA fragments. So to keep this simple we're going to ignore all that, and consider only us diploid eukaryotes, where the question of chromosome numbers becomes a real issue.

Normally, I'd be scribbling madly on a whiteboard, so we'll have to make do with some scribbles on the computer screen. Here, for instance, is a typical cartoon chromosome. It's a string of DNA, and scattered along it we have sequences for genes, that I've labeled "A", "B", "C", "D", and "E". I've also drawn a circular blob in the middle: that's important. It's not a gene, it's a structure called the centromere, which gets all wrapped up in proteins to form a kinetochore. It's a sort of anchor point; when the cell needs to move chromosomes around, as it does during cell division, it hitches motor proteins to the kinetochore and using drag lines called spindle fibers, tows it to a new destination.

I mentioned that this was a diploid organism — that just means that every chromosome comes in pairs. This cell would have a similar chromosome to the one that has the ABCDE genes on it; here I've draw it as containing the same genes, but in slightly different forms: abcde. This matters because during meiosis, when gametes (sperm and egg) are formed, the two chromosomes line up with one another and the cell machinery tows one chromosome to one daughter cell, and the other to the other daughter cell. It's accounting; it makes sure each daughter gets a copy of all of the genes, one A or one a, one B or one b, etc., for instance.

For now, put the fact that there are two copies of each chromosome at the back of your mind and don't worry about it. Let's think about a single chromosome and ask what can happen to it.

Here's something fairly common. An error in copying the DNA can lead to the loss of a piece of DNA. This happens with a low frequency, but it does happen — if we sequenced your DNA, we might well find a few bits missing here and there. We can get situations like this, where a whole gene gets lost.

Don't panic! Remember that we have two copies of every chromosome, so while this one is missing the "D" gene, there's that other chromosome floating around with a "d" gene. This is not necessarily bad for the individual, it just means he doesn't have a spare any more.

Another kind of error that can happen with a low frequency is a duplication, where the machinery of the cell accidentally repeats itself when copying, and you get an extra copy of a piece of a chromosome, like so:

This person has two copies of D on this chromosome now (and remember that other chromosome, with it's d gene — he actually has 3 copies in total now). This is not usually harmful: it gives the individual a little extra redundancy, and that's about it. It can change the total amount of the D gene product in the cell, and if it's a gene for which precise dosage is important, it can have visible effects…but in most cases, this is a neutral change.

You may have noticed that nothing has changed the chromosome numbers yet. Here's a situation that can lead to the formation of a new chromosome: what if there is a duplication of the centromere, rather than a gene?

Remember, I told you that the centromere/kinetochore is where the cell attaches lines and motors to haul the chromosome to the appropriate daughter cell. In this case, two lines are attached; what if one tries to pull one centromere to the left, and the other tries to pull the other centromere to the right? Tug of war!

The end result is that the chromosome is broken into two chromosomes. I think this is a key concept that the questioner is missing: chromosome numbers really aren't significant at all! You don't need to add significant new information to create a new chromosome, and as I'll show you in a moment, a reduction in chromosome numbers does not represent a loss of genetic information. Chromosome are disorganized filing cabinets, nothing more; we can shuffle genes around between them willy-nilly, and the cell mostly doesn't care. A fission event like the one described above basically does nothing but take one pile of genes and split them into two piles.

But there are some important effects. This may not be an entirely neutral situation. Let's bring back that abcde chromosome, and pair it up with our two new chromosomes, AB and CDE.

The accounting is accurate. This cell has two copies of the A gene, an "A" and an "a", just like normal, and the two new chromosomes can still pair up efficiently with the old chromosome in meiosis, just like before. This is a healthy, functioning, normal cell, except for one thing: if it goes through meiosis to make a sperm or egg, it's going to make a larger number of errors. There are three centromeres there, to be split into two daughter cells! Never mind what the Intelligent Design creationists tell you — the cell is really, really stupid, and it will more or less decide by eeny-meeny-miny-moe how to divvy up those chromosomes. If by chance the split is that one daughter gets AB + CDE, and the other gets abcde, both daughters have the full complement of genes and all is well. However, the split could also be that one daughter gets AB and nothing else, while the other gets CDE + abcde … and that's no good. One is missing a whole bunch of genes, and the other has an overdose of a bunch.

The net result is that although this individual is fine and healthy, a significant number of his or her gametes may carry serious chromosomal errors, which means they may have reduced fertility. They aren't sterile, though; some of their gametes will have the full complement of genes, and can similarly produce new healthy individuals who will probably have fertility problems. (Note: the significance of those fertility problems will vary from species to species. Organisms that rely on producing massive numbers of progeny so that a few survive to adulthood would be hit hard by a change that cuts fecundity; species that rely on producing a few progeny that we raise carefully to adulthood, like us, not so much. So you have to have sex 20 times to successfully produce a child instead of 5 times; that won't usually be a handicap.)

So our two chromosome individual will have a reduced fertility as long as he or she is breeding with the normal one chromosome organisms, but those split chromosomes can continue to spread through the population. They are not certain to spread — they're more likely to eventually go extinct — but by chance alone there can be continued propagation of the two chromosome variant. Which leads to another misconception in the question: something doesn't have to provide a benefit to spread through a population! Chance alone can do it. We don't have to argue for a benefit of chromosome fission at all in order for it to happen.

So we can have a population with a low frequency of scattered chromosomal variants, some carrying the rare two chromosome variant and others the more common one chromosome form. What if two individuals carrying the two chromosome variant breed? They can produce offspring that look like this:

How many centromeres are there? Four, not three. This is a situation the cell machinery can handle reliably, and this individual will consistently produce good gametes that accurately carry AB + CDE, nothing more, nothing less, and will have no reduction in fertility. Now we have a potentially interesting situation: individuals with the one chromosome situation have full fertility when breeding with other individuals with one chromosome; individuals with two chromosomes have full fertility when breeding with other individuals with two chromosomes; it's when individuals with two different chromosome arrangements try to breed that fecundity is reduced. This is a situation where speciation is a possibility.

One last thing: what about reducing chromosome numbers? That's easy, too. Here's an organism with an AB chromosome, and a different chromosome with the genes MN on it. They can simply fuse in the region of the centromere.

This happens with a low frequency, too, and has been observed many times (hint: look up Robertsonian fusions on the web.) I think the key issue to understand here is that chromosome number changes are typically going to represent nothing but reorganizations of the genes — the same genes are just being moved around to different filing cabinets. This has some consequences, of course — you increase the chances of losing some important file folders in the process, and making it more difficult to sort out important information — but it's not as drastic as some seem to think, and chromosome numbers can change dramatically with no obvious effect on the phenotype of the organism. These really are "small adaptations over time", or more accurately, "small changes over time", since there is no necessary presumption that these are adaptive at all.

I've discussed fusion events and how they relate to evolution before, and there's an interesting difference in context there, too. My prior article was a response to Casey Luskin, an ignorant creationist who used his misunderstanding of genetics to foolishly assert the existence of a major problem, and that's where we have a conflict: ignorance is not a problem, but stupidly using your ignorance to push invalid ideas is. This question in my mailbox is also ignorant — the fellow really doesn't understand the basics of genetics — but it's self-recognized ignorance that, in a good way, prompts him to ask a sincere question.

If you want to dig a little deeper, there are many ways genetic information can be rearranged on chromosomes, and this has opened the doors to some interesting evolutionary research. I've described how we can map the reshuffling of chunks of genetic information over time, a process called synteny mapping, which allows us to reconstruct ancestral chromosomes. A fish might have 42 chromosomes, and we might have 46, but we can still trace how the ancestral arrangement was scrambled in many different ways to generate the modern arrangements.