Genetic continuity and change among the Indigenous peoples of California

Prior to colonialism, California harbored more language variation than all of Europe, and linguistic and archaeological analysis have led to many hypotheses to explain this diversity 1. We report genome-wide data from 80 ancient Californians and 40 ancient northern Mexicans dating to 7400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on California’s Northern Channel Islands and the adjacent Santa Barbara mainland coast from 7400 BP to modern Chumash groups represented by individuals who lived around 200 BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5200 BP, documenting northward migrations that are candidates for spreading Uto-Aztecan languages prior to the dispersal of maize agriculture from Mexico 2-4. Baja Californians share more alleles with the earliest Central Californian in the dataset than with later Central Californians, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions 1,5. After 1600 BP, ancient Channel Islanders lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.