After 1769, the life of the California natives who came in contact with the Spanish was reshaped by the mission fathers, not the townspeople of the pueblos or the soldiers of the presidios. The Franciscans came to California not merely to convert the tribes to Christianity but to train them for life in a European colonial society. Conversion was seldom an entirely voluntary process, and converts (neophytes) were not left to return to their old ways but were required to live in the walled mission enclosure or on rancherías, separate settlements sponsored by missions located some distance from the mission proper. There they were taught Spanish as well as the tenets of their new religion and trained in skills that would equip them for their new lives: brickmaking and construction, raising cattle and horses, blacksmithing, weaving, tanning hides, etc.
In theory, the neophytes were to live at the missions only until this process of education was complete, and then they would establish homes in the nearby pueblos. As the native people of one region were Christianized and educated, the missionaries were to move on, leaving the old missions behind to become parish churches as they built new missions in more distant locations peopled by non-converted tribes or "gentiles." In fact, neither the Spanish government nor the Franciscans ever judged any of the neophytes ready for "secularization" or life outside the mission system, and Christian natives or "Mission Indians" and their descendants remained at the missions until the system was abolished in 1834.
By that time, sixty-five years of exposure to Europeans had reduced the number of California's native peoples by half to about 150,000. Although outright warfare cost few lives, Spaniards had introduced not only Christianity but also new diseases to which the neophytes had no resistance, and thousands died in epidemics. Crowded, harsh living conditions at the missions contributed to the Indians' health problems, and infant mortality and death rates among young children soared. It was the tribes of the coast, the "Mission Indians," who were most drastically affected. Tribes like the Modocs in the northern mountains had little or no contact with the Spanish and suffered little.