NEW YORK (NYT NEWS SERVICE ).- The remains of three people were uncovered during excavation work at the Alamo in San Antonio, and the discovery has reignited longstanding disputes over how to tell the full history of one of the most fabled battle sites in the United States.

The findings, announced by state officials on Dec. 13, came in the early stages of a major renovation of the former Spanish mission. Now, some San Antonio residents and members of Native American groups are calling for the project to be paused.

The remains appeared to be the bodies of an infant, a young adult or teenager, and an adult. It was still unclear who they were and when they died. While excavation in pits where the remains were found had been halted, the renovation was still moving forward.

But the $450 million project, which involves restoring the oldest buildings and repurposing others to serve as a visitors center and museum, has been fraught with disagreements over how best to accommodate tourists while respecting the Alamo’s complex history — and about whose stories have been venerated and whose have been forgotten.

Ramon Vasquez, a member of the Alamo Citizens Advisory Committee and the Tap Pilam Coahuiltecan Nation, said the Alamo was home to San Antonio’s oldest cemetery, where more than a thousand people, most of them indigenous, were buried centuries ago.

But he said officials in charge of the renovation had not done enough to recognize that burial ground. “They have fought us very hard not to call it a cemetery,” he said.

For decades, Vasquez and his family have lobbied local officials to recognize and devote resources to the study of the burial ground. He said the recent discoveries of human remains were not publicized until he submitted public records requests.

The state’s General Land Office manages the Alamo, which includes a church, a barracks and a plaza, and has denied that claim. It said it had followed the protocol for dealing with human remains and alerted the public two days after archaeologists determined that the bodies were purposely buried in the church.

“The GLO has long recognized the Alamo as a burial ground and will ensure that this history is told in the future museum,” Karina Erickson, a spokeswoman for the office, said.

“A carnival-like atmosphere has plagued this sacred ground for years,” she added. “Today, double-decker buses drive across the battlefield and mission footprint where descendants of all backgrounds lived, worked and died. The Alamo plan does not erase history; instead it aims to tell it.”

Erickson said the land office works with representatives of federally recognized Native American tribes (the Tap Pilam Coahuiltecan Nation is not federally recognized) and that the Alamo’s philosophy was “that the most respectful treatment of human remains is to leave them in place whenever possible.”

In U.S. history books, the Alamo was most closely associated with the 1836 Battle of the Alamo in which Texians (settlers who lived in Texas when it was a part of Mexico) fought to protect their garrison for 13 days before they were defeated and killed by Mexican soldiers.

“Remember the Alamo!” became a battle cry during Texians’ subsequent battles for independence from Mexico and throughout the Mexican-American War, a war that ended with the U.S. acquisition of Mexican territory extending from Texas to the Pacific Ocean.

But before it became an artifact of Anglo expansionism, the Alamo was known as the Misión San Antonio de Valero, a mission populated mainly by Spanish priests and indigenous people who had converted to Christianity.

Vasquez said historical documents suggested that more than 1,300 people had been buried there, most of whom were members of indigenous tribes, and some appeared to have been of African or European descent.

“You’re talking about liberty, American history and perseverance,” he said. “This site is the epitome of the American story, even prior to 1836, when you have a whole hundred years of history of people who contributed to the city of San Antonio and to the state of Texas.”

He said the borders of the cemetery would probably include the ground the church sat on and would fan out from there. More study is necessary to find out exactly what the borders were before the renovation proceeds, he added.

At a public meeting in San Antonio on Wednesday, the city’s Historic and Design Review Commission voted 7-4 to approve plans for the first phase of the renovation, even though some attendees raised concerns about the cemetery.

Gabriel Velasquez, a member of the commission, voted against the plan. “This is probably the most significant cemetery in the history of the state of Texas,” he said Friday, adding that it represents one of the continent’s earliest examples of the conversion of indigenous people to Christianity.

The Texas Historical Commission recognized the burial ground as a “historic Texas cemetery” in July. It does not come with the same protections as a “state antiquities landmark” designation, which the Alamo has.

The remains were discovered in late November and early December. The infant and adult were found in the nave, or main area, of the church. The young adult or teenager was found in the Monks Burial room, which is also in the church building.

The General Land Office said it was not surprised by the discoveries, which happened during efforts to install moisture-monitoring equipment and document the foundations of the structures. It added that human remains had been found at the Alamo in 1989 and 1995.

In September, the Tap Pilam Coahuiltecan Nation and other plaintiffs filed a federal lawsuit against San Antonio, the land office, its commissioner, George P. Bush, and others, arguing that the people in charge of the renovation had neglected to properly study and protect the burial ground.

Other groups have raised their own concerns about the renovation from various personal and political angles, including some who want to preserve the focus on Texian heroism.

The buildings at the Alamo are crumbling, and officials want to redesign the historical plaza to make the site more engaging for visitors. But given that so many groups are worried, Velasquez said they should take more time to think things through.

“The constant struggle between Catholics and Protestants and Mexicans and Anglos — all of that historic racism and discrimination is embodied in this situation that’s going on today,” he said.

“We see that there’s something wrong with this process,” he added. “This is not about stopping it. This is about doing it right.”

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