So that's part 1. Please ask me if you have any problems or questions. And also ask me if you need references, and I will be happy to provide.
2. How we get whole new branches to the tree of life.
As you can see, new species always evolve very gradually, almost imperceptibly. It's only species that emerge, never a sudden big change like sprouting a wing or anything.
We did 5000 years. Now project another 5000 years. Now you've got another new species or two, Littlefishius thuggius and so forth. One is an inch long, etc. etc. One gives birth to live young, etc., but they're still pretty similar. Now go 500,000 years. You've had a million generations. You've got like ten different species. By this time the original Littlefishius heneni is extinct. (Most species go extinct. 99% of all species ever have gone extinct.) One of your groups that branched off from Group B, call it Group B(1), is 6" long, bears live young, is orange with a single black spot, and eats other smaller fish, and some other stuff. At this point, Biologists say, "Hold everything. This is more different than just a new species. At this point, I think we better call it a new genus. Let's call it Mediumfishius cutieus.
So that's how we get new species and new genii. They always branch off from existing species. They never emerge as a huge break from anything. Everything's very gradual. You never really see the difference, but gradually new species, genii, families, emerge this way, each one branching off of an existing species. By the time we see the new species, most of its ancestral species are extinct.
Do you understand all this? Have any problem with it?