Two weathered gravestones sit in a small, dusty rectangle in front of the grand Spanish church at the heart of the nation’s newest World Heritage Site, the San Antonio Missions. I’ve been to Mission San Jose many times — to attend the lively Mariachi Mass, to photograph its antique majesty, to reflect on the history of this place and its role in the settlement of the American Southwest. But this is the first time I’ve thought of it as a cemetery.

I’m seeing it through the eyes of two direct descendants of the missions’ original inhabitants, members of the Tap Pilam Coahuiltecan Nation, whose ancestors inhabited this part of what is now Texas for thousands of years. Some 300 years ago, they helped to build these missions, and their descendants maintain a vital connection to them.

Last year the five missions, spread out over about 12 miles along the San Antonio River, became the first U.S. World Heritage Site to be named in 20 years. Four of them are still active Catholic parishes, attended by some of the original Native American descendants; the fifth, Mission San Antonio de Valero, went on to become a military garrison — the legendary Alamo, now converted into a memorial to the battle fought there.

Ramón Vásquez, a straight-talking Texan with a dark ponytail, and the soft-spoken Jesús “Jesse” Reyes Jr., an anthropologist in a cowboy hat and bolo tie, are my guides today. Ramón, executive director of a nonprofit organization called the American Indians in Texas, has teamed up with Jesse to create Yanawana Mission Tours — named for the pre-Hispanic name for the San Antonio River — which offers an eye-opening perspective not just on the missions, but also on American history itself.