title: Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication.
abstract: The complex evolutionary history of maize (Zea mays L. ssp. mays) has been clarified with genomic-level data from modern landraces and wild teosinte grasses [1, 2], augmenting archaeological findings that suggest domestication occurred between 10,000 and 6,250 years ago in southern Mexico [3, 4]. Maize rapidly evolved under human selection, leading to conspicuous phenotypic transformations, as well as adaptations to varied environments [5]. Still, many questions about the domestication process remain unanswered because modern specimens do not represent the full range of past diversity due to abandonment of unproductive lineages, genetic drift, on-going natural selection, and recent breeding activity. To more fully understand the history and spread of maize, we characterized the draft genome of a 5,310-year-old archaeological cob excavated in the Tehuacan Valley of Mexico. We compare this ancient sample against a reference panel of modern landraces and teosinte grasses using D statistics, model-based clustering algorithms, and multidimensional scaling analyses, demonstrating the specimen derives from the same source population that gave rise to modern maize. We find that 5,310 years ago, maize in the Tehuacan Valley was on the whole genetically closer to modern maize than to its wild counterpart. However, many genes associated with key domestication traits existed in the ancestral state, sharply contrasting with the ubiquity of derived alleles in living landraces. These findings suggest much of the evolution during domestication may have been gradual and encourage further paleogenomic research to address provocative questions about the world's most produced cereal.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Electronic address: jramos@lcg.unam.mx.
authors.forename: Jazmín
authors.initials: J
authors.lastname: Ramos-Madrigal
authors.affiliation: Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10(th) and Constitution Avenue, Washington, DC 20560, USA; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
authors.forename: Bruce D
authors.initials: BD
authors.lastname: Smith
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: J Víctor
authors.initials: JV
authors.lastname: Moreno-Mayar
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Shyam
authors.initials: S
authors.lastname: Gopalakrishnan
authors.affiliation: Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, 1 Shields Avenue, Davis, CA 95616, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Ross-Ibarra
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA 6102, Australia; NTNU University Museum, 7491 Trondheim, Norway.
authors.forename: M Thomas P
authors.initials: MTP
authors.lastname: Gilbert
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Electronic address: wales.nathan@gmail.com.
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D012641:Selection, Genetic; D003313:Zea mays / Q000235:genetics*
chemical_list: D018744:DNA, Plant
keywords: Zea mays; ancient DNA; archaeobotany; archaeology; domestication; maize; paleogenomics; teosinte