The last two decades have seen important advances in our knowledge of maize domestication, thanks in part to the contributions of genetic data. Genetic studies have provided firm evidence that maize was domesticated from Balsas teosinte (Zea mays subspecies parviglumis), a wild relative that is endemic to the mid-to lowland regions of southwestern Mexico. An interesting paradox remains, however: Maize cultivars that are most closely related to Balsas teosinte are found mainly in the Mexican highlands where subspecies parviglumis does not grow. Genetic data thus point to primary diffusion of domesticated maize from the highlands rather than from the region of initial domestication. Recent archeological evidence for early lowland cultivation has been consistent with the genetics of domestication, leaving the issue of the ancestral position of highland maize unresolved. We used a new SNP dataset scored in a large number of accessions of both teosinte and maize to take a second look at the geography of the earliest cultivated maize. We found that gene flow between maize and its wild relatives meaningfully impacts our inference of geographic origins. By analyzing differentiation from inferred ancestral gene frequencies, we obtained results that are fully consistent with current ecological, archeological, and genetic data concerning the geography of early maize cultivation.T he geography of origins and diversification of agricultural species has important implications for unraveling the ecological context of Neolithic societies and for understanding current patterns of diversity in domesticated plants and animals. Traditionally the realm of archeology and botany (1, 2), the study of plant domestication has seen important contributions from genetics during the last two decades (3). Genetic data often provide evidence that is hard to obtain by other means, making it an invaluable complement to other lines of inquiry.As a case in point, molecular markers were instrumental in establishing the single domestication of maize (Zea mays subspecies mays) from an extant wild relative (4, 5). Maize was shown to originate from annual teosinte (Zea mays subspecies parviglumis, hereafter parviglumis) around 9,000 y B.P., placing domestication in the mid-to lowland regions of southwest Mexico where parviglumis grows endemically. As predicted by this result (6), excavations in the heart of parviglumis' distribution have produced the earliest (8,700 y B.P.) phytolith evidence for maize cultivation (7). Other finds from Tabasco (7,300 y B.P.) (8) and Panama (7,400 y B.P.) (9) also support an early presence of maize throughout the Meso-American lowlands.Although different types of evidence seemingly concur, questions nonetheless remain about the interpretation of the genetic data. While unequivocal with respect to maize's wild ancestor, marker evidence suggests that maize from the Mexican highlands, rather than from the lowlands, is most closely related to parviglumis and appears to have given rise to all cultivars currently grown throug...

To better understand the range of adaptation of maize (Zea mays L.) landraces, climatic adaptation intervals of 42 Mexican maize races were determined. A database of 4161 maize accessions was used to characterize altitudinal and climatic conditions where the 42 maize races grow, yielding ecological descriptors for each race. Using the geographical coordinates of the collection sites of each accession, their climatic conditions were characterized using the geographic information system IDRISI and a national environmental information system. Analyses of variance and cluster analyses of the racial ecological descriptors were performed to determine possible environmental groupings of the races. We found a very high level of variation among and within Mexican maize races for climate adaptation and ecological descriptors. The general overall climatic ranges for maize were 0 to 2900 m of altitude, 11.3 to 26.6°C annual mean temperature, 12.0 to 29.1°C growing season mean temperature, 426 to 4245 mm annual rainfall, 400 to 3555 mm growing season rainfall, and 12.46 to 12.98 h mean growing season daylength. These climatic ranges of maize surpass those from its closest relative, teosinte (Z. mays ssp. parviglumis Iltis and Doebley), indicating that maize has evolved adaptability beyond the environmental range in which ancestral maize was first domesticated.

Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. On the basis of single-nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified an 50-Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures .700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Z. mays subspecies parviglumis and mexicana and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few crossover-induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.T HE evolutionary role of chromosomal inversions has been studied in a wide array of organisms, from insects (Ayala et al. 2011;Stevison et al. 2011) to birds (Huynh et al. 2011) and plants (Hoffmann and Rieseberg 2008; Lowry and Willis 2010). Examination of inversion polymorphism was fundamental to the early study of selection and adaptive diversity, as well as the basis for understanding the maintenance of neutral polymorphism within populations (Dobzhansky 1950;Hoffmann et al. 2004). Homologous pairing of an inverted and a noninverted chromosome in heterozygotes leads to the formation of an inversion loop, and crossing over in an inversion loop can cause the formation of a dicentric chromosome and an acentric fragment at meiosis I, resulting in terminal deletions of the affected chromosome and gamete death at frequencies that correlate with the size of the inversion (Burnham 1962). Because of the difficulty of homologous pairing and the deleterious effects of homologous crossing over in inversions, inversions are typically observed to disrupt recombination in heterozygous individuals, leading to measurable effects on nucleotide sequence polymorphism, including the generation of extended linkage disequilibrium (LD). Inversion-induced LD has been reported in a variety of organisms, including humans (Bansal et al. 2007), Drosophila subobscura (Munte et al. 2005), and several other species (reviewed in Hoffmann and Rieseberg 2008). Strong differentiation between chromosomal arrangements (as measured by F ST ) has also been used as evidence of inversions in Drosophila (Andolfatto et al. 1999;Depaulis et al. 1999;Nóbrega et al. 2008).A variety of circumstances can favor the maintenance or spread of an inversion polymorphism. The inversion may be 2010), ...

Adaptation of crops to climate change has motivated an increasing interest in the potential value of novel traits from wild species; maize wild relatives, the teosintes, harbor traits that may be useful to maize breeding. To study the ecogeographic distribution of teosinte we constructed a robust database of 2363 teosinte occurrences from published sources for the period 1842–2016. A geographical information system integrating 216 environmental variables was created for Mexico and Central America and was used to characterize the environment of each teosinte occurrence site. The natural geographic distribution of teosinte extends from the Western Sierra Madre of the State of Chihuahua, Mexico to the Pacific coast of Nicaragua and Costa Rica, including practically the entire western part of Mesoamerica. The Mexican annuals Zea mays ssp. parviglumis and Zea mays ssp. mexicana show a wide distribution in Mexico, while Zea diploperennis, Zea luxurians, Zea perennis, Zea mays ssp. huehuetenangensis, Zea vespertilio and Zea nicaraguensis had more restricted and distinct ranges, representing less than 20% of the total occurrences. Only 11.2% of teosinte populations are found in Protected Natural Areas in Mexico and Central America. Ecogeographical analysis showed that teosinte can cope with extreme levels of precipitation and temperatures during growing season. Modelling teosinte geographic distribution demonstrated congruence between actual and potential distributions; however, some areas with no occurrences appear to be within the range of adaptation of teosintes. Field surveys should be prioritized to such regions to accelerate the discovery of unknown populations. Potential areas for teosintes Zea mays ssp. mexicana races Chalco, Nobogame, and Durango, Zea mays ssp. huehuetenangensis, Zea luxurians, Zea diploperennis and Zea nicaraguensis are geographically separated; however, partial overlapping occurs between Zea mays ssp. parviglumis and Zea perennis, between Zea mays ssp. parviglumis and Zea diploperennis, and between Zea mays ssp. mexicana race Chalco and Zea mays ssp. mexicana race Central Plateau. Assessing priority of collecting for conservation showed that permanent monitoring programs and in-situ conservation projects with participation of local farmer communities are critically needed; Zea mays ssp. mexicana (races Durango and Nobogame), Zea luxurians, Zea diploperennis, Zea perennis and Zea vespertilio should be considered as the highest priority taxa.

Societal Impact Statement Crop wild relatives (CWR) are plant taxa closely related to crops and are a source of high genetic diversity that can help adapt crops to the impacts of global change, particularly to meet increasing consumer demand in the face of the climate crisis. CWR provide vital ecosystem services and are increasingly important for food and nutrition security and sustainable and resilient agriculture. They therefore are of major biological, social, cultural and economic importance. Assessing the extinction risk of CWR is essential to prioritise in situ and ex situ conservation strategies in Mesoamerica to guarantee the long‐term survival and availability of these resources for present and future generations worldwide. Summary Ensuring food security is one of the world's most critical issues as agricultural systems are already being impacted by global change. Crop wild relatives (CWR)—wild plants related to crops—possess genetic variability that can help adapt agriculture to a changing environment and sustainably increase crop yields to meet the food security challenge. Here we report the results of an extinction risk assessment of 224 wild relatives of some of the world's most important crops (i.e. chilli pepper, maize, common bean, avocado, cotton, potato, squash, vanilla and husk tomato) in Mesoamerica—an area of global significance as a centre of crop origin, domestication and of high CWR diversity. We show that 35% of the selected CWR taxa are threatened with extinction according to The International Union for Conservation of Nature (IUCN) Red List demonstrates that these valuable genetic resources are under high anthropogenic threat. The dominant threat processes are land use change for agriculture and farming, invasive and other problematic species (e.g. pests, genetically modified organisms) and use of biological resources, including overcollection and logging. The most significant drivers of extinction relate to smallholder agriculture—given its high incidence and ongoing shifts from traditional agriculture to modern practices (e.g. use of herbicides)—smallholder ranching and housing and urban development and introduced genetic material. There is an urgent need to increase knowledge and research around different aspects of CWR. Policies that support in situ and ex situ conservation of CWR and promote sustainable agriculture are pivotal to secure these resources for the benefit of current and future generations.