Zoo officials removed the cub while Ya Ya was asleep. They reported that the mother panda searched for her cub after waking and then fell into what onlookers described as a a state of depression.
In the wild, pandas are totally dependant on their mothers for the first few months of their lives. Cubs live with their mothers for about a year and a half, when females often conceive again.
It's unknown whether Ya Ya's second cub will be reunited with its mother.
Panda Baby Boom
Historically, captive breeding of pandas has been difficult.
Females and males are only able to breed for a few days each year, so two animals must be brought together at exactly the right time.
"There's a lot of knowledge necessary to make that happen," the San Diego Zoo's Penny said.
Problems persist after conception.
Washington's National Zoo is still celebrating the birth of a male cub, Tai Shan, which arrived on July 9. He now weighs 65 pounds (30 kilograms) and is doing well, but he is a rarity.
The zoo's five previous cubs, born to the famous Hsing-Hsing and Ling-Ling between 1983 and 1989, all died before they were four days old.
"The first one died of pneumonia, and the second was stillborn," zoo spokesperson Pepper Long said.
"Then a pair of twins died, one from lack of oxygen and the other of infection. The fifth cub died of pneumonia just 23 hours after birth."
Wild panda breeding is difficult to study, because the animals are so reclusive. But long-term data on some populations suggest wild pandas have relatively high reproductive rates.
Captive facilities say that they have acquired the knowledge to close the gap.
"We've worked with the Chinese, shared information, and I think we've all learned a lot in the past ten years, as shown by the increased number of [captive born] giant panda babies," Penny said.
China's Wolong center has experienced the largest baby boom. Dozens of the endangered animals have survived in recent years. Last month four sets of twins were born at the facility.
The births have boosted China's number of captive pandas to over 180. Last spring the animal known as Xiang Xiang became a pioneer as the first captive-born giant panda to be released into the wild (watch video of the release and see photo).
And Ya Ya's sad tale comes on the heels of happy news for her wild cousins.
A recently completed study by Chinese and British scientists suggests that there could be twice as many wild pandas as previously believed. A 2004 Chinese government census estimated only 1,596 animals, but recent research suggests that up to 3,000 pandas could be roaming the wilderness.
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