On a rugged coastal bluff overlooking Tomales Bay is the site of a former Coast Miwok village that tells a remarkable story about Native American resilience in the face of oppression.

There, amid the biting winds and foggy mists at Toms Point in Marin County, are buried obsidian and chert cutting tools, animal remains, and other signs of indigenous life long after the Spanish missions closed down and the American frontier was settled.

The presence of these artifacts is evidence, archaeologists say, that native people in Northern California carried on their traditions and maintained tribal ties much longer than many historians thought.

“It’s a story of continuity and change and persistence that hasn’t been told before,” said Tsim Schneider, an assistant professor of anthropology at UC Santa Cruz, who is himself a tribal member and contends that the cultural and spiritual legacy of the Miwok lives on today. “It’s not a story of loss or acculturation.”

Schneider’s findings at Toms Point, a spectacularly rugged promontory at the edge of the ocean, contradicts the standard narrative that all California Indians were killed off or held captive in colonial missions, and later rancherias and reservations.

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Schneider and Lee Panich, an associate professor of anthropology at Santa Clara University, based their findings on excavations of three Miwok village sites in Marin County.

Toms Point, now managed by Audubon Canyon Ranch, was especially interesting, Schneider said, because Coast Miwok villages thrived at least 4,000 years before a Boston sailor named George Thomas Wood jumped ship and established a trading post there in the mid-19th century.

With the help of ground-penetrating radar, Schneider and Panich found artifacts of daily and ritual life by Miwok and Southern Pomo Indians at Toms Point after it became a trading post. They also consulted work done in the area in the early 1900s by UC Berkeley anthropologists and U.S. Office of Coast Survey maps drawn in 1856 and 1862.

Their analysis of seeds, charred plant remains, obsidian projectile points, grinding stones, nails, shells, fish, pig bones, ceremonial artifacts and several items from an 1852 shipwreck in Tomales Bay paint an illuminating picture of a troubling, little-known period in the history of the natives in Northern California.

The studies, which are referenced in several recent scientific papers, show that the local Indians adapted their diets and lifestyles to the American frontier, but also maintained many of their ancient traditions and practices.

“We see evidence that they applied traditional skills to imported materials,” said Schneider, noting excavations of weapons, tools and jewelry made of glass, scavenged metal and, in one case, an old Champagne bottle. “Native people were still engaging with their world. There was still a presence and a connection to their ancestral homeland and to familiar landscapes.”

The fate of the Bay Area Indian population is important because the region was a fertile hunting ground and popular location for large villages before Europeans arrived.

The Coast Miwok and Southern Pomo settled on the north side of the bay, establishing major villages throughout Marin and Sonoma counties. They were mostly along a trail skirting the bay that eventually became Highway 101, but also along the many rivers and bays on the north coast.

The shells and artifacts the Indians discarded built up over thousands of years into huge mounds that, 100 years ago, could be found all around San Francisco Bay.

More than 400 mound sites, known as middens, have been recorded in Marin County, including one in Larkspur that archaeologists excavated for the first time in 2014, revealing a treasure trove of Coast Miwok life dating back 4,500 years.

That 300-foot-long site contained human remains, a ceremonial California condor burial, musical instruments, throwing sticks from a time before the introduction of the bow and arrow, and the bones of about 100 grizzly and black bears, the largest collection ever found in a prehistoric site in the Bay Area.

But the rich Native American culture that once existed in the Bay Area was mostly destroyed during the Mission era, from 1769 to the 1830s. The Franciscan missionaries relocated many native residents of Marin County to San Francisco’s Mission Dolores, which was established in 1776.

Then, in the early 1800s, Mission San Rafael was built in response to the establishment of Fort Ross, a Russian mercantile colony near present-day Jenner, and many of the Native Americans who agreed to convert to Christianity were sent out to work at various enterprises around Northern California.

The studies of Toms Point show it was a refuge for Coast Miwok — and probably Southern Pomo, Wappo and Ohlone as well — after the missions closed. Many of the natives from the area worked in the 1840s and 1850s at a hide and tallow business started by Wood, who deserted either a whaling or military ship in the 1840s and became known as Tom Vaquero — thus the name of the point where he established his business.

Wood not only sold hides to ships traveling the coast of California, he also evidently loaned out Indian labor to inland farms and Russan River logging operations. He even married a Coast Miwok woman from Tomales Bay.

Schneider’s research shows that the Miwok in the area, which they called Segloque before the 1840s, continued many of their traditions, including hunting elk, gathering acorns, conducting mortuary rites and holding night dances, even as European trading and customs took hold.

Native traditions and cultural practices also continued for many decades at many other sites around the Bay Area, including Rancho Nicasio, in West Marin, and Olompali, near the Petaluma River.

“There are probably countless sites like this where Native Americans returned and re-established their identities — places where Coast Miwok may have intermarried with other tribal people.” said Schneider, one of 1,100 members of the Federated Indians of Graton Rancheria, who traces his own ancestry to an interracial union in the 1840s in Bodega Bay.

Schneider said today’s descendants of the Miwok and Pomo still fish, collect shellfish and dive for abalone — all practices reflected in the archaeological record at Toms Point.

Native people also continue to make clamshell bead necklaces, which were traditionally used as money by the Coast Miwok. Flintknapping, or carving tools out of obsidian, chert and even bottle glass, is another tradition seen at Toms Point that is still practiced by native descendants.

“Being able to fashion a projectile point from a piece of obsidian and a colorful shard of bottle glass is something in which I find deep meaning,” Schneider said. “This is a traditional practice that is being maintained by numerous tribal citizens, and we continue to braid this traditional technology into our own sense of identity and connections to place and history.”

He acknowledged that the story of Toms Point is one of exploitation and discrimination, but said it is also one of hope in the enterprising spirit and resilience of Native American culture.

“Despite California’s very destructive form of colonization, they are still here, still speaking their languages, still practicing their dances,” Schneider said. “The missions are gone, but Coast Miwok people are still here.”

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite