On some phylogenetic trees, you'll see that dates indicate when things last shared a common ancestor, when those splits occurred on the phylogenetic tree. So how do they get those dates? Well, you can do it using the fossil record, but that's not how it's done on most phylogenetic trees. Usually, you're using this concept of the molecular clock. Now you're probably going to be responsible for this concept.
It's unlikely that you need to actually calculate dates using a molecular clock, but you want to understand just generally how this works. So sort of fundamentally, what we're going to say here is that the number of mutations between taxa right? Number of mutations between taxa, you could say lineages or species, whatever. The number of mutations can estimate the date of divergence, or in other words, when those taxa last shared a common ancestor.
So why does this work? It works because mutations tend to enter populations at a relatively constant rate. Right? Mutations, it well, mutation is a random process, but over a long period of time, that means that randomness kind of evens out and it becomes quite predictable how often mutations are going to happen. Now we're going to say here that this is especially true for neutral mutations, and we're going to come back to that in a little bit as to why that's important.
But to explain this, I have this graph here, and you can see on the y-axis we have the number of mutations, and on the x-axis we have time. So each dot here is supposed to represent the comparison of 2 species, and you can see that if it's been not that long a time since they last diverged, well, there aren't that many mutations. And as you go up over time, right, the longer it's been since the divergence, the more and more mutations there have been. And then you can see there's sort of some scatter around the line. It's not a perfect relationship, but we can calculate this mutation rate.
And if we know that mutation rate, well, then we can take 2 species, and we can just say, well, how many mutations have there been? We can figure that out. We can sort of draw across to the line, and that'll tell us, that's about how long it's been since they shared a common ancestor. Now this all hinges on, though, us knowing that mutation rate. So how do we calculate the mutation rate?
We're going to say we can compare the DNA sequences of related species with known dates from the fossil record. Alright. So we're going to calibrate this using fossils. So we're going to look at lions and tigers here, and we're just going to imagine that we have a really good fossil record for when they last shared a common ancestor. So if we know when that last common ancestor lived pretty darn precisely from the fossil record, that gives us the time.
Well, then we just have to calculate the mutations, count the number of mutations for some section of DNA between these organisms, do some simple division, and that gives us our mutation rate. Now we can apply that mutation rate to other species that we don't have the good fossil record for. Alright. Now this works, and it works pretty darn well, but we just need to be a little bit careful here. We just want to say that molecular clocks are only estimates, and there are a few reasons here.
Mutation rates, well, they can differ in different lineages. Right? Mutations are random, so there's just going to be some random difference between different lineages. Now that you should be able to account for by just, you know, putting error bars on whatever your date is, you know, understanding that you're calculating a range, an estimate, not a precise date. But in very different lineages, the mutation rate can fundamentally differ.
Right? You don't want to use a mutation rate from bacteria to calculate the date of the split in big cats. Right? These are just very different organisms that almost certainly just have fundamentally different mutation rates. Now we also want to say that you can't calibrate your clock beyond the time of a good fossil record.
Right? You need fossils to do this. And a fossil record is only good for the last 500 million years or so, ago, back to about the Cambrian. So this just really actually doesn't work very well for deep time at all. And if you have lineages where you don't have a good fossil record, well, it's much harder to calculate that mutation rate.
And then finally, we're going to say here that natural selection can influence the clock. Right? So I'm going to go back up over here again to this idea of it being especially true for neutral mutations. That's because a neutral mutation, natural selection doesn't affect. So that new mutation, whether it sticks around in the population, that's again just going to be random chance.
Well, natural selection is going to influence that random chance, whether or not those new mutations stick around. It may make it that new mutations are more likely to stick around or much less likely to stick around, and that's going to drastically affect the rate of mutations entering your population, and that affects how you calculate the clock. So sometimes people come up with estimates that are actually quite wrong because the section of DNA they were looking at, they, for whatever reason, didn't understand that it was under strong natural selection. Alright. So we do just want to say, though, this does usually work pretty darn well, as long as you're willing to accept sort of a range of dates, and that's because mutations do enter populations at relatively constant rates over time, and we can use that to calculate those dates of divergence.
Alright. We'll practice this a little bit more. We'll see you there.
