In terms of actual, hard paleontological and archaeological evidence, there is no disagreement amongst the scientific community that Homo sapiens originated in Africa.
This has nothing to do with the fact that three of the modern species of great ape, which are also the three which are most closely genetically linked to modern humans are found in Africa. This is strong corroborating evidence, but it is the actual physical bones and tools of early humans that are first found in Africa.
This also takes place LONG after the break up of Pangea. A map of the Earth at the time would look pretty much exactly the same as it does now. The main differences would be on the coast lines, where differences in sea levels during glaciations or in inter-glacial periods would reveal or conceal large sections of coastal real estate.
The African origin of humans is also evidenced in mitochondrial DNA studies and other projects mapping the human genome and regional variations. The greatest genetic diversity among all human populations occurs amongst African peoples. Genetic comparisons between groups such as the San and !Kung tribes of the Kalahari, the Mbutu tribes of the Congo basin, and populations in East and West Africa show more genetic variability than exists between Asians, North American Indians and Europeans. This indicates that Africa was the site of the original development of the human population, and that all the other groups of human 'races' are actually descended from just one group of the diverse African genetic mileau (the East African branch actually).
Yes, that means that if you were able to trace back through the family trees you would find that the Grand Wizard of the KKK is actually more closely related to the Masai warriors of Kenya than Oprah Winfrey is (who is of West African descent).
From Africa, humans spread out all over the globe, crossing land bridges and sailing across stretches of water to reach Australia at least 45,000 years ago (by the Upper Swan River near Perth, as well as the Willandra lakes region in the southern interior by 40,000 years ago), and crossing the Beringia land bridge exposed between Alaska and Russia to colonize North America about 12,000 years ago.
The only debate in scientific circles is whether there was one or several migrations of humans out of Africa. The first anatomically modern humans (Homo sapiens sapiens) appear in South Africa, at the cave complex of Klasies River Mouth by 100,000 years ago. After that, the same phenotypic subspecies, with a distinctive round cranium, thin walled skull, lack of a strong brow ridge and a protruding chin (also known as a mental eminence) started appearing in the Middle East, Europe and Asia.
Some indicate that this suggests that anatomically modern humans arose in South Africa, and spread out once again from there to take over or intermingle with all of the populations of earlier Homo sapiens (such as the Neandertals) that had migrated out of Africa. There are others who have proposed a 'regional continuity' model, where the populations of Homo sapiens that had moved out of Africa and into Europe and Asia somehow totally independently for some reason developed the exact same phenotypic changes in morphology seen in the South African population, and Homo sapiens sapiens evolved throughout the entire range of the species. No one has yet managed to propose a viable mechanism for this unusual pattern of evolution. It has always seemed to me to be a vaguely racist hypothesis, as if even scientists are unwilling to accept the evidence that all humans could possibly have come from Africa THAT recently.
Strong, independent physical evidence comes from the fields of palaeontology, archaeology, geology, biogeography, and genetics that humans definitely originated in Africa, and moved out from there to colonize the rest of the world. There is also evidence that it happened as many as three times.