For societies with writing systems, hereditary leadership is documented as one of the hallmarks of early political complexity and governance. In contrast, it is unknown whether hereditary succession played a role in the early formation of prehistoric complex societies that lacked writing. Here we use an archaeogenomic approach to identify an elite matriline that persisted between 800 and 1130 CE in Chaco Canyon, the centre of an expansive prehistoric complex society in the Southwestern United States. We show that nine individuals buried in an elite crypt at Pueblo Bonito, the largest structure in the canyon, have identical mitochondrial genomes. Analyses of nuclear genome data from six samples with the highest DNA preservation demonstrate mother–daughter and grandmother–grandson relationships, evidence for a multigenerational matrilineal descent group. Together, these results demonstrate the persistence of an elite matriline in Chaco for ∼330 years.

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Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago 1 – 3 . We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work 4 , we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500–1500 and a maximum of Ne=1530–8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large 5 – 6 . Confirming a small, interconnected Ceramic Age population 7 , we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically-differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world 1 , 8 .

Maize is a cultigen of global economic importance, but when it first became a staple grain in the Americas, was unknown and contested. Here, we report direct isotopic dietary evidence from 52 radiocarbon-dated human skeletons from two remarkably well-preserved rock-shelter contexts in the Maya Mountains of Belize spanning the past 10,000 years. Individuals dating before ~4700 calendar years before present (cal B.P.) show no clear evidence for the consumption of maize. Evidence for substantial maize consumption (~30% of total diet) appears in some individuals between 4700 and 4000 cal B.P. Isotopic evidence after 4000 cal B.P. indicates that maize became a persistently used staple grain comparable in dietary significance to later maize agriculturalists in the region (>70% of total diet). These data provide the earliest definitive evidence for maize as a staple grain in the Americas.

Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.