When Shea Homes dug up about 500 bodies to make way for a road through its new Trilogy subdivision, the developer set in motion a governmental process steeped in confidentiality.
State policymakers have spent years fine-tuning what must be done after such discoveries, but many tiptoe around volatile questions.
"The politics are interesting and are such that it behooves me not to say too much," said Adrian Praetzellis, a Sonoma State anthropologist who studies American Indian remains.
State laws require landowners to contact California's Native American Heritage Commission when native remains are found. The commission then assigns a person known as the "most-likely descendant" to consult with the landowner.
But there's sometimes tenuous or no ancestral ties between the "descendant" and the uncovered bodies, scientists and American Indians said. Many remains found in eastern Contra Costa and Alameda counties, for example, are too old to be linked directly with any modern tribes.
The dilemma gained prominence in 2004 when a federal appeals court ruled that9,300-year-old remains found in Washington could not be traced to a modern group. The decision allowed scientists to study "Kennewick man" and set a precedent that has yet to play out in state courts.
Praetzellis and other researchers said it is more important for American Indians to be involved in the moving of ancient remains than to force them to prove a genetic link after being left out entirely for decades.
"They just have to say, 'Yeah, I feel culturally connected to those remains,'" said Jeff Fentress, a San Francisco State anthropologist. "It is really up to that person to determine how to handle that burial."
Representatives of Shea Homes said they could not answer most questions about the remains found on their site, where jewelry, bone and stone tools, arrowheads and other artifacts also were found. Others were simply unwilling.
An archaeologist working for Shea Homes, Miley Holman, said Fentress would be researching the bodies and artifacts found in Brentwood. But Fentress said he did not know who was studying the remains, leaving it unclear where 500 ancient bodies had gone.
San Francisco State anthropology professor Mark Griffin also declined to comment "for reasons of confidentiality, propriety, due process, site protection and security."
The American Indians involved with the Brentwood dig and other excavations were more willing to talk about their experiences.
For the approximately 350 people on the state's list of most-likely descendants, the benefits extend beyond the cultural. In some cases, a descendant stands to gain hundreds of dollars in consulting fees when called in to supervise a project.
While state law does not require landowners to pay descendants, many agencies or developers choose to pay the native representative rather than a separate consultant. Fees can range from $15 per hour to more than $100.
Lathrop resident Ramona Garibay, the most-likely descendant who oversaw the Brentwood dig, said her interest in American Indian history prompted her to get her name on the Native American Heritage Commission list. The state register says Garibay is affiliated with Ohlone, Miwok and Patwin tribes.
"I thought it was very interesting because I knew nothing about my ancestors," she said. "I just go out there and make sure the burials are respected."
But Garibay's experience also points out a frame of mind that has split some American Indian groups: Is it OK to move remains for the sake of a strip mall or luxury homes, even if they will be reburied nearby?
"It's sad to see them disturbed, but yet it's kind of exciting because I'm learning a lot of stuff," she said. "I'm all for the history. I wasn't brought up with the myths about burial sites like other Native Americans."
Others disagree. They say even the oldest American Indians were buried for spiritual reasons and should not be disturbed.
The Brentwood remains have been in the same place for up to 7,000 years. They should have been left there, said Joan Villa, a leader of one faction of the fractured Ione Band of Miwok Indians in the Central Valley.
"They destroyed a burial mound of the ancient Windmiller people," she said. "We would have never agreed to the desecration of such a large mound."
The state commission is responsible for determining which tribes have links to each part of California. Debbie Treadway, a scientist with the agency, said she often consults the Smithsonian Institute's "Handbook of North American Indians" to make such decisions.
In Brentwood, Treadway said, the commission usually assigns a Bay Miwok to a burial site even though it's difficult to tell who the true descendants are in eastern Contra Costa County.
But the most-likely descendant list has rankled some native groups. Villa said she should have been the one to oversee the Brentwood project but has been left off the state list for political reasons.
Treadway, with the commission, said tribes make the political decisions.
"The tribe makes the decision on who it wants on the list," she said.
While the most-likely descendant list requires discussions between property owners and American Indians, landowners have the final say on how best to protect remains if they do not agree with the descendant.
The state process generally works out amicably, but some researchers say the potential for abuse exists. With ancient remains being found repeatedly in Brentwood, including on a proposed college site across the road from the Trilogy tract, the issue is likely to come up again soon in Contra Costa County.
And then there is the Kennewick man court ruling, which divided the research community.
Among the scientists who cringed was Praetzellis, the Sonoma State anthropologist. It's time governments gave American Indians the benefit of the doubt, he said.
"This is just another stone thrown at the Indians," he said. "Cooperation is the only way to go."