Changing the number of individuals per taxa/species affect the hybridisation of result

[fam yiqing]

Hi

I have run SNaQ once and I got result A

After that I have increase two individuals of one certain species and the result totally changes.

And I try to randomly take three individuals from that particular species, the result change again.

May I know if the number of individual per taxa/species gonna affect the result?
Thank you very much