I am trying to test if the sequences for a certain species in my dataset can be considered monophyletic or not. I have multiple sequences per species in the dataset like so :

species 1 : - seq 1.1 - seq 1.2 - seq 1.3

species 2 : - seq 2.1 - seq 2.2 - seq 2.3

species 3 : - seq 3.1 - seq 3.2 - seq 3.3

To test monophyly i want to put a hard constraint on the sequences of species one and compare it to the negative constraint like so:

constraint species1 = seq 1.1 seq seq 1.2 seq 1.3

constraint species1neg negative = seq 1.1 seq seq 1.2 seq 1.3

Now if the marginal likilihood of the H1 hypothesis is higher than the negative constraint one does this mean my species is likely monophyletic? (using stepping stone method) Or could it still be the case that some of the sequences in species one do not belong there?

Thanks for your help.