title: The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding.
abstract: Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens dating at a similar age of 5,300-4,970 calibrated y B.P. On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, we show herein that the earliest maize from San Marcos cave was a partial domesticate diverging from the landraces and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci, such as teosinte branched1 (tb1) and brittle endosperm2 (bt2), had already lost most of the nucleotide variability present in Balsas teosinte, others, such as teosinte glume architecture1 (tga1) and sugary1 (su1), conserved partial levels of nucleotide variability that are absent from extant maize. Genetic comparisons among three temporally convergent samples revealed that they were homozygous and identical by descent across their genome. Our results indicate that the earliest maize from San Marcos was already inbred, opening the possibility for Tehuacán maize cultivation evolving from reduced founder populations of isolated and perhaps self-pollinated individuals.
authors.affiliation: Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico.|Grupo de Interacción Núcleo-Mitocondrial y Paleogenómica, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico.
authors.forename: Miguel
authors.initials: M
authors.lastname: Vallebueno-Estrada
authors.affiliation: Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico.
authors.forename: Isaac
authors.initials: I
authors.lastname: Rodríguez-Arévalo
authors.affiliation: Grupo de Interacción Núcleo-Mitocondrial y Paleogenómica, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Rougon-Cardoso
authors.affiliation: Instituto Nacional de Antropología e Historia, CP 06100 Mexico DF, Mexico.
authors.forename: Javier
authors.initials: J
authors.lastname: Martínez González
authors.affiliation: Instituto Nacional de Antropología e Historia, CP 06100 Mexico DF, Mexico.
authors.forename: Angel
authors.initials: A
authors.lastname: García Cook
authors.affiliation: Grupo de Interacción Núcleo-Mitocondrial y Paleogenómica, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico; vielle@cinvestav.mx rafael.montiel@cinvestav.mx.
authors.forename: Rafael
authors.identifier: 0000-0001-8052-0679
authors.initials: R
authors.lastname: Montiel
authors.affiliation: Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Irapuato, 36821 Guanajuato, Mexico; vielle@cinvestav.mx rafael.montiel@cinvestav.mx.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vielle-Calzada
mesh_terms: D001106:Archaeology; D000071278:Domestication; D014644:Genetic Variation; D018745:Genome, Plant; D007178:Inbreeding; D008800:Mexico; D003313:Zea mays / Q000235:genetics*
keywords: Tehuacán; domestication; maize; paleogenomics; teosinte