By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.

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The turkey (Meleagris gallopavo) was independently domesticated in Mesoamerica and the Southwest, the latter as the only case of Native American animal domestication north of Mexico. In the upland (non-desert) portion of the American Southwest, distinctive closely related mtDNA lineages belonging to haplogroup H1 (thought to indicate domestication) occur from ca. 1 A.D. (Basketmaker II period) through early historic times. At many sites, low frequencies of lineages belonging to haplogroup H2 also occur, apparently derived from the local Merriam’s subspecies. We report genetic, stable isotope, and coprolite data from turkey remains recovered at three early sites in SE Utah and SW Colorado dating to the Basketmaker II, III, and early Pueblo II periods. Evidence from these and other early sites indicates that both the H1 and H2 turkeys had a predominantly maize-based diet similar to that of humans; prior to late Pueblo II times, the birds were kept primarily to provide feathers for blankets and ritual uses; and ritualized burials indicate turkeys’ symbolic value. We argue that viewing individuals from the H1 and H2 haplogroups as “domestic” versus “wild” is an oversimplification.

Four separate lines of evidence show that the Cedar Mesa Basketmaker II were dependent on maize horticulture: the settlement pattern of the mesa-top Basketmaker II; stable carbon-isotope analysis of Basketmaker and other skeletal remains from the Cedar Mesa area; and two different analyses of coprolites and midden constituents from the Turkey Pen Cave site (a Basketmaker II site in Grand Gulch, which drains parts of Cedar Mesa). All of these analyses concur with a dependence on maize horticulture for the Cedar Mesa Basketmaker II, a dependence not differing significantly from later Pueblo inhabitants of Cedar Mesa and elsewhere. Whether other Basketmaker II variants were as reliant on maize is uncertain, but there are good indications that at least some, and probably all, were. By 2,000 years ago the Basketmaker II peoples on Cedar Mesa were not modified hunters and gatherers, but relied on maize.

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