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Scientists researching the periods before written historical records were made have established that the territory of what is now referred to generically as South Africa was one of the important centers of human evolution. It was inhabited by Australopithecines since at least 2.5 million years ago. Modern human settlement occurred around 125,000 years ago in the Middle Stone Age, as shown by archaeological discoveries at Klasies River Caves.[8] The first human habitation is associated with a DNA group originating in a northwestern area of southern Africa and still prevalent in the indigenous Khoisan (Khoi and San). Southern Africa was later populated by Bantu-speaking people who migrated from the western region of central Africa during the early centuries AD.

Professor Raymond Dart discovered the skull of a 2.51 million year old Taung Child in 1924, the first example of Australopithecus africanus ever found. Following in Dart's footsteps Robert Broom discovered a new much more robust hominid in 1938 Paranthropus robustus at Kromdraai, and in 1947 uncovered several more examples of Australopithecus africanus at Sterkfontein. At the Blombos cave in 2002, stones were discovered engraved with grid or cross-hatch patterns, dated to some 70,000 years ago. This has been interpreted as the earliest example ever discovered of abstract art or symbolic art created by Homo sapiens.[9]

Many more species of early hominid have come to light in recent decades. The oldest is Little Foot, a collection of footbones of an unknown hominid between 2.2 and 3.3 million years old, discovered at Sterkfontein by Ronald J. Clarke. An important recent find was that of 1.9 million year old Australopithecus sediba, discovered in 2008. In 2015, the discovery near Johannesburg of a previously unknown species of Homo was announced, named Homo naledi. It has been described as one of the most important paleontological discoveries in modern times.[10]