“Beautiful, isn’t it?” he said.

The scientists also found a profusion of animal fossils at the site — saber-toothed cats, mongooses, wild dogs, antelopes and hyenas, among others. Dr. Berger and Paul Dirks, a geologist at James Cook University in Queensland, Australia, hypothesized that the animals might have been lured to the edge of a 100- to 150-foot funnel-shaped shaft into a deep cave, perhaps by the scent of water during a drought, then plunged to their deaths.

Image Matthew Berger, 11, was nine when he stumbled into a major archeological discovery. Credit... Benedicte Kurzen for The New York Times

There is evidence that maggots and carrion beetles, but not carnivores, fed upon the rotting carcasses, leading the scientists to conclude that the carnivores, too, must have died from the fall. The first downpours of the rainy season may have swept the bodies into a pool of water rich with lime and sand — the ingredients of cement — that essentially froze them in place. Dr. Berger called the sediba fossils “a time machine” into evolutionary processes.

Researchers now think the split between apes and the hominid lineage occurred around seven million years ago in Africa. The sparse fossil record shows early hominid species already walking upright, but still relatively apelike. Small australopithecines, with bodies and brains not much bigger than those of modern chimpanzees, were widespread from 3.8 million to three million years ago, most famously Australopithecus afarensis like Lucy.

Just when changes leading to Homo were happening remains unclear in the fossil record. Hominids started shaping stone tools about 2.6 million years ago. Hominids identified as Homo appeared more than two million years ago, their direct ancestry anything but clear. The species Australopithecus sediba thus shared a time with Homo habilis and Homo erectus.

Ian Tattersall, a paleoanthropologist at the American Museum of Natural History in New York, supported the discovery team’s interpretation of the fossils as a previously unclassified species of advanced Australopithecus “with suggestions of Homo.”

But it is often a toss-up whether a fossil discovery will bring order or confusion to the family tree. William H. Kimbel, director of the Institute of Human Origins at Arizona State University, said the fossil remains were instead a species of early Homo with some cranial and skeletal material “seen otherwise only in Homo.”

As the taxonomic debate continues, so, too, does fossil hunting at the Malapa site. So far, the scientists exploring it have not even started digging, but have cleared it of rubble left by men mining for lime, probably about a century ago, and other debris. They keep finding more hominid bones that click together like pieces of jigsaw puzzles. Since submitting the paper to Science in November, they have found at least two more individuals, one an infant.