Making a phylogenetic tree

Image: Pixabay

I thought I’d take a moment to discuss how exactly biologists create phylogenetic trees. Our discussion will not include factors such as morphological comparisons etc.- which was more widely used before genetics came along- but rather the molecular methods used today. I thought this would be better served as a blog post rather than a podcast episode, as in blog format I can use images to illustrate what I’m saying (which is predictably rather difficult in audio format!).

So, let’s say that you’re an ecologist who’s just discovered an uninhabited island far out to sea. There’s three species of snake on this island (hence the picture at the top) and you want to know how long ago these species diverged from their common ancestor. You find a fossil which tells you that species A and species C must have diverged 15 million years ago, but you can’t find anything for the other species. So, instead, you sequence a protein common to all species (let’s say haemoglobin for the sake of argument) which gives you the results in Table 1. How does this help you?

Table 1: The number of amino acids in the protein we’re sequencing that are different between each of the three snake species.

Looking at our table, you can see that, in 15 million years, there have been thirty amino acid sequence changes between species A and species C. However, this doesn’t quite give us our rate of mutation yet. To know why this is the case, you’ve got to consider that both species have been evolving away from their common origin. This means that we’ve effectively got to double the time between them to 30 million years. After all, species A has been evolving for 15 million years and species C has been.

This means that, if we assume a constant mutation rate, we end up with a rate of 1 mutation per million years. What we’ve done is calibrate our molecular clock- we now know the rate of mutation for the protein we’re using to build our tree.

So, let’s now look at the difference between species B and species C, which is also 30 mutations. This means that these two species also had a total evolution time of thirty million years. Dividing by two, we get a divergence time of 15 million years, as with species A. By contrast, species A and species B have eleven amino acid differences, meaning that they must have diverged 5.5 million years ago.

How does all of this fit together? Well, A and B must have diverged after both the A-C divergence or the B-C divergence. This means that C must have split off from the common ancestor first, and then A and B diverged, as shown below:

Figure 1: The phylogenetic tree you end up with as a result of our reconstruction. Time is shown (not to scale) along the bottom)

Of course, there are some assumptions we’ve made while constructing our tree, such as a constant rate of mutation. Added to this, most phylogenies will be a lot more complicated than just three species. However, it serves well as an example of the process by which such tree are constructed. A more in-depth discussion of these assumptions, as well as the process of speciation itself, is a story for another time.

The perspective shift of evolution

Image: Pixabay

I just wanted to share something that I’ve recently been delving into a bit more thanks to my studies- namely, the age of the Earth people commonly accepted before the theory of evolution as proposed by Darwin and Wallace in 1859 came along. I thought it might give some idea of how big a shift in perspective would have been needed for the average person back in 1859.

So, how old was the Earth commonly accepted to be? Well, it was mostly calculated using the generations and ages listed in the Bible. There’s a YouTube video published in 2020 which uses the chronology to calculate that, if people used the text literally, the world would have been thought to have been created in 4163 BCE.

The chronology that I think is most often cited is that of James Ussher, an Irish bishop. His date is 4004 BCE, which indicates that a sort of consensus appears to be forming between these old thinkers that the Earth was perceived to be roughly six thousand years old.

Consider, then, the contrast between this number and the age of the Earth which we’ve calculated today- about 4.54 billion years. Let’s suppose we make the number calculated by Ussher (5863 years old in 1859) equivalent to one step (which I’m going to approximate as a metre for the sake of my calculations). To walk this new age of the Earth, you would have to travel over 774 kilometres- very roughly 484 miles. For context, Google maps tells me that’s a longer journey than driving from Portsmouth to Edinburgh.

None of this is to say that the theory proposed isn’t correct- there’s a wealth of biological evidence to back it up. However, I find myself agreeing with the sentiment I saw expressed by Stephen Jay Gould– just because their ages of the Earth turned out to be wrong, doesn’t mean that we should deride the people behind it for that.