Due to whatever factors induce speciation (distance apparantly being one of them), visits between boyfriends and girlfriends of these creatures (all living in a state of grace), could be few and far between, but just as fertile as ever upon appropriate consumation ~ male on top, lady on the bottom eh?!
So, they go on like this for one of God's near eternities, swapping genes, but still growing apart. Group A could have more visits with Group C than with Group B or Group D. Etc.
Finally, one day God (or whoever) decides "I'm creating four new species), and it's done, but some are more closely related to others ~ yet deletions and insertions may be identical, or different in major ways (affecting body shape, color, etc.)
It all makes sense.
This stuff isn't as linear as it might at first appear ~ the changes affect groups over long periods of time in many generations.