Hi Clifton,
Back to your example, with P being the parent species and C1 and C2 its children.
P: S=23; D=6; L=6
C1: S=24; D=5; L=6
C2: S=23; D=2; L=3
When P speciates, there are 23 gene copies in its genome (S=23). D=6 is irrelevant for the children, because the duplications happened before the speciation (the number S=23 is a consequence of the 6 speciations). L=6 means that there are 6 losses to distribute between C1 and C2 (which is counter-intuitive and that I maybe want to change in a next release). In this example, 4 out of the 6 losses will happen along C1, and 2 along C2.
Right after P speciates, C1 has 23 gene copies. Then
there are 5 duplications (D=5 for C1) and 4 losses (4 out of the 6
that are indicated in P). This results in 23+5-4=24 gene copies when C1
speciates (S=24 for C1 ok!)
Right after P speciates, C2 has 23 gene copies. Then
there are 2 duplications (D=2 for C2) and 2 losses (2 out of the 6
that are indicated in P). This results in 23+2-2=23 gene copies when C1
speciates (S=23 for C2 ok!)
This indeed deserves some explanation in the wiki... But as I said, I'll need more time, because I think this will be better with figures.
I hope this answer your questions
Best,
Benoit