Documenting ancient diffusion routes of domesticates and how they were modified when introduced into new regions has long been a challenge. For example, hybridization and gene flow have long confounded attempts to understand the origins of either indica rice8 in the Indian subcontinent or maize in southern Mexico9. The origin and adaptation of maize in the US Southwest is a similarly difficult case. Following its initial domestication from the wild grass teosinte in southern Mexico10,11, maize diffused throughout the Americas, spreading through much of the continental United States after its introduction to the Southwest around 4,100 calendar years before present (BP)7. There has been considerable debate about the arrival of maize into the Southwest, however, as early archaeological samples suggested a highland route5,6, whereas more recent samples1,2 and morphological similarity to extant Mexican maize support a lowland, Pacific coast route3,4. And while temporal variation in Southwest maize cob morphology has been described2, the genetic changes responsible for adaptation to the Southwest environment during the last 4,000 years are still uncharacterized.
Maize was faced with a number of environmental challenges upon arrival in the Southwest, from extreme aridity to new dietary preferences7. Our population-level samples corresponding to temporally distinct occupations of the same cave site (Tularosa cave: SW2K, n = 10; SW750, n = 12), combined with published genomic data of the maize progenitor Z. m. parviglumis (Supplementary Table 4), allow us to distinguish evidence for these more recent adaptations from selection that occurred during maize domestication. We first used the population branch statistic PBS18 to identify genes with the highest dissimilarity between teosinte and our ancient Southwest landraces (Fig. 2a). These genes were likely to be early targets of maize domestication that preceded arrival in the Southwest. Many of these genes also show a very negative Tajima's D, consistent with the effects of strong selection (Fig. 2a), and seven of the top ten genes (Supplementary Table 1) are located in previously identified selected regions19. The top gene, zagl1, corresponds to a MADS-box transcription factor associated with shattering, a key domestication feature strongly selected for by human harvesting20. Several other genes are also well known for their roles in domestication: ba1 has a major role in the architecture of maize21, zcn1 and gi are associated with the regulation of flowering20,22 and tga1 controls the change from encased to exposed kernels23.
The study of domestication and early crop evolution has largely been limited to the identification of key phenotypic, morphological and genetic changes between extant crops and their wild relatives. As demonstrated here, the application of new paleogenomic approaches to well-documented temporal sequences of archaeological assemblages opens a new chapter in the study of domestication: it is now possible to move beyond a simple distinction of ‘wild’ versus ‘domesticated’29,30 and track sequence changes in a wide range of genes over the course of thousands of years.
Just think, none of us would be here if our Native American's had not done what they did in those early times. Hybridization of these early maize or corn plants brought the possibility of you and I to life.
I am just "amaized."