The origin and evolution of maize in the American Southwest

Abstract

Maize offers an ideal system through which to demonstrate the potential of ancient population genomic techniques for reconstructing the evolution and spread of domesticates. The diffusion of maize from Mexico into the North American Southwest (SW) remains contentious with the available evidence being restricted to morphological studies of ancient maize plant material. We captured 1 Mb of nuclear DNA from 32 archaeological maize samples spanning 6000 years and compared them with modern landraces including those from the Mexican West coast and highlands. We found that the initial diffusion of domesticated maize into the SW is likely to have occurred through a highland route. However, by 2000 years ago a Pacific coastal corridor was also being used. Furthermore, we could distinguish between genes that were selected for early during domestication (such as zagl1 involved in shattering) from genes that changed in the SW context (e.g. related to sugar content and adaptation to drought) likely as a response to the local arid environment and new cultural uses of maize.

The interplay of demography and selection during maize domestication and expansion

“…Support is also found for mexicana introgression in the southwestern US at specific chromosomal regions such as a putative inversion polymorphism on chromosome 3 (Figure 2). These results confirm previous findings suggesting maize from the highlands of Mexico originally colonized the southwestern US [35]. The more limited signal of mexicana introgression here may be due to subsequent gene flow from lowland maize as suggested by [35].…”

“…These results confirm previous findings suggesting maize from the highlands of Mexico originally colonized the southwestern US [35]. The more limited signal of mexicana introgression here may be due to subsequent gene flow from lowland maize as suggested by [35]. Very little evidence is found for mexicana haplotypes extending into South America, as highland-adapted haplotypes would likely have been maladaptive and removed by selection as maize traversed the lowland regions of Central America ([49]).…”

“…All individuals from both the Mexican and Guatemalan highlands exhibited highly significant evidence for shared ancestry with mexicana (Figure S5A). Maize from the southwestern US also showed more limited evidence of introgression, consistent with findings from ancient DNA suggesting this region was originally colonized by admixed maize from the highlands of Mexico [35]. In contrast, the distribution of z-scores for South American populations overlapped zero, providing no evidence for spread of mexicana haplotypes to this region.…”

Reconstructing ancient genomes and epigenomes

“…Although most paleogenomic studies have focused on a limited number of individuals, current approaches allow the characterization of genome-wide SNP variation at ancient population scales 71,111 . Future studies can be expected to investigate genetic variation in large population samples on the high-density SNP or even whole-genome scale, thus improving our understanding of past demographic, adaptive and admixture trajectories with greater detail 112 .…”

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces

“…Given its history, maize is an ideal model system to study parallel adaptation. Maize was first domesticated in the warm lowlands of the Balsas River Valley approximately 9,000 years ago [16,17], and subsequently spread to several independent highland regions, first to the the Mexican Central Plateau, and then to the highlands of the southwestern United States, Guatemala and the Andes [18,19,20,21,22,23,24,25,26,27,28,29]. While highland regions colonized by maize are far from identical, commonalities include a shorter growing season, low temperature, low partial pressure of atmospheric gases, and high ultraviolet radiation [30,31].…”