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The infant ape’s life was brief, running out before the age of 2. Yet its discovery 13 million years later by a team led by Bay Area anthropologist Isaiah Nengo is casting light on a shadowy and pivotal period in prehuman history.

Characteristics of the fossil, the most complete extinct ape skull ever found, mark it as a new species in the great flowering of ape evolution, which later led to the emergence of humans. We didn’t descend from the little ape; rather, we have kin in common.

“Together, we have great-great-great-great grandparents that we all share,” said Nengo, who lives in Ross, digs in Kenya and teaches at Cupertino’s De Anza College. His research, published in Wednesday’s issue of the prestigious journal Nature, was funded by the San Francisco-based Leakey Foundation, founded to explore the origins of humanity.

Little is known about ancient apes, the ancestors of living apes and humans.

It was a time of great evolutionary success, with an explosion of genetic diversity. And then the apes mysteriously declined. Only a few remained, in restricted places: gibbons and orangutans in Asia and chimps, gorillas and the early human australopithecines in Africa.

In contrast, monkeys prevailed. And humans, for better or worse, are extraordinarily successful.

The 13-million-year-old fossil, now extinct, reveals what the common ancestor of all living apes and humans may have looked like. Dating back to the Miocene, its species has been named Nyanzapithecus alesi.

We branched off quite recently, only 6 to 7 million years ago.

The stunning discovery in 2014 came at the end of a long and disappointing day near the western shore of Kenya’s Lake Turkana in Africa’s Great Rift Valley, in a place full of volcanic rock and largely devoid of fossils, said Nengo.

Nengo was deeply invested in the success of the project at the Turkana Basin Institute. He had secured grant funding, assembled the team, coordinated the effort and was responsible for everything from fuel in trucks to water in jugs.

“We spent the whole day finding nothing. Zero. We were in a pretty bad mood,” he recalled. So the team gave up and went back to camp for dinner, walking the familiar route they had always taken, back and forth, every day.

An assistant, John Ekusi, pulled out a cigarette. “We told him: ‘You’re going to kill us! Smoke it far away,’ ” Nengo said. So Ekusi walked ahead of the team, about 500 yards.

Then Ekusi suddenly stopped, looking down, intently. He spotted something in the rock — the leg bone of an elephant, perhaps?

“We rushed to where he was, yelling ‘What did you find?’ and we knew right away it was super special,” said Nengo. Taking out a brush, he whisked away dirt. “We instantly knew it was a cranium, with an eye socket in front. It was extremely well preserved.”

Anthropology is a profession that usually works with mere fragments. “It was incredibly shocking,” he said.

But they were running out of daylight. So the team re-buried the fossil, returned to camp and waited for the sun to rise. “It was a terrible night,” he laughed.

Starting at 5 a.m. the next day, they excavated a block of rock around the fossil, then drove it back to a larger supply campsite, where it could be safely transported to a lab. (Its name is taken from an African word for ancestor “ales.” Fondly, Nengo’s team calls it “Alesi.”)

Alesi’s skull is about the size of a lemon. With a small snout, it resembles a baby gibbon. No one knows if it was male or female, or how it died.

Because the most informative parts of the skull are preserved inside the fossil, Nengo enlisted the help of an extremely sensitive form of 3D X-ray imaging at the synchrotron facility in Grenoble, France.

“We were able to reveal the brain cavity, the inner ears and the unerupted adult teeth with their daily record of growth lines,” said Paul Tafforeau of the European Synchrotron Radiation Facility, in a prepared statement. “The quality of our images was so good that we could establish from the teeth that the infant was about 1 year and 4 months old when it died.”

The unerupted adult teeth indicated that the specimen belonged to a new species, never before seen.

Its bony ear tubes are an important feature linking it with living apes, according to Ellen Miller of Wake Forest University. But the region of the inner ear responsible for balance reveals that it was not agile and acrobatic in trees, like gibbons. Instead, Alesi likely moved more cautiously, according to Fred Spoor of the Max Planck Institute of Evolutionary Anthropology.

What became of its family? Perhaps they went extinct due to competition with monkeys or other apes. Or maybe the environment changed, and they couldn’t adapt. Once rich with trees, the Great Rift Valley is now a vast arid region.

The discovery of Alesi — the base of our ancestral tree — is life-altering for Nengo, who for 14 years has commuted 120 miles, four days a week, to teach at De Anza College.

He’s been offered a three-year contract, and perhaps tenure, with New York’s Stony Brook University, which runs the Turkana Basin Institute. Stony Brook is an international center of excellence in research and training in paleontology and paleoanthropology, specifically in the areas of primate and human evolution.

He was inspired to study human evolution as a high school student in Kenya, when he heard a talk by famed paleoanthropologist Richard Leakey. Nengo earned his Ph.D. at Harvard, where he met, fell in love and married language specialist Ann Robyns, whose family has lived in Marin County since the mid-1950s. They moved to Ross to be near her family and raise their three children.

Ultimately, he landed at De Anza, calling it “a remarkable place, which really believes in encouraging any student, regardless of background, to pursue the sciences.” The De Anza Foundation raises funds to send students, many of whom have never traveled overseas, to join Nengo in fossil prospecting, cleaning, excavation, measurement, identification and photography.

Soon he’ll return to Kenya to search for more fossils.

His discovery of Alesi adds a big new piece to the puzzle of primate evolution. But it also poses poignant questions: Why did its species perish? Is this a clue to the declining empire of apes?

“It is one of the biggest evolutionary mysteries that we need to resolve,” he said.

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