Our example asks, based on the data below, which two species do you think are sister taxa? All right. So we have this character matrix here, and in our character matrix, we're looking at 10 different nucleotides here as our characters, and we have an outgroup, and then we have 3 taxa here, taxa Q, taxa R, and taxa S in our ingroup. Alright. So just remember, how do we figure out what our sister taxa?

Alright. So we have to figure out between taxa Q, R, and S, which one of those share the most derived characters. Right? Remember when I did this previously, I had a little table to do that. I'm not going to draw the table.

I'm just going to write every pairwise comparison. We have to count how many are shared between Q and R, how many are shared between Q and S, and how many are shared between R and S. Those are all the possible sharings that there could be. And now I'm just going to go through each nucleotide, decide if it is a shared derived character, and if it is, which taxa share it? And I'll just put a little tally mark next to the sort of pairwise comparisons that I have if it's shared between those two.

Alright. So let's start. Number 1, is that a shared derived character? It's not. Right?

So those characters are different from the outgroup, but none of them are shared. So I can basically just ignore nucleotide 1. What about nucleotide 2? Alright. These are shared, and they are different from the outgroup, but they're shared between all of these.

So, it's actually not very helpful. It's not going to help me make a group within my ingroup, to link anything else. Now I'll still just go ahead and put tally marks there, but I'm going to put a tally mark, Q and R, show you that, Q and S, share that, R and S share that. Again, it's not going to help me very much in the end. Alright.

But we can keep going. Nucleotide 3 here. What about nucleotide number 3? Is that a shared derived character? It is.

Right? These C's are shared, and they're different from the outgroup. So that means that I can put a tally mark next to Q and R, because they share that shared derived character, so it gets a tally mark there. Alright. What about nucleotide 4?

Yeah. Nucleotide 4, taxon R and S have that shared G character, and that's a derived character. So I'm going to put a tally mark here next to taxon R and S. They have a shared derived character between them. What about nucleotide 5?

Right. Well, those C's are a shared derived character because it's shared between Q and R, and it's different from the outgroup. So Q and R get another tally mark there. What about 6 here? Alright.

Number 6 is the same thing as nucleotide 2. They it is shared. It doesn't give me much information though, because it's shared between all of them, but I'll go ahead and put a tally mark. It doesn't hurt. All right.

We then have nucleotide 7 here. Is this a shared derived character? Well, yes, it is because the C's are different from the G, and it is shared between taxon Q and R. So Q and R now get another tally mark. They're starting to rack them up here.

What about 8? All right. Not a shared derived character. There is nothing shared about those characters. They are all different.

What about nucleotide 9 here? Well, nucleotide 9, you see that the T's are shared between Q and S, and that's different from the outgroup. So I'm going to put a tally mark next to my Q and S comparison here. And then finally, what about 10?

Oh, yeah. 10 shows me that Q and R have that shared derived character that is different from the outgroup, so it gets another tally mark. Alright. So what are Sister Taxa? Well, Sister Taxa here are the ones with the most shared derived characters, and that would be taxa Q and R.

I'm going to assume that they are a group because I'm going to assume that the majority of those shared characters shared derived characters are homologous traits, and I'm going to link them together on my phylogenetic tree. Now these other ones have shared derived characters, but remember some of these could be analogous traits. And that's why we try and get lots and lots of characters, because in the end, the most of them will be homologous, and the biggest number is going to win out. Alright.

So Q and R, that's my answer.