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In 2012 we initiated a new series of excavations in Tehuacán caves with the purpose of uncovering organic remains corresponding to ancient Mesoamerican crops.

Our reexamination of San Marcos cave yielded several macrospecimens of maize dating 5,300–1,950 calibrated y B. Using whole-genome shotgun sequencing, we characterized the genome of three specimens dating 5,300–4,970 y B. and corresponding to the earliest cultural phase of Tehuacán.

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To determine the genomic constitution and degree of genetic variability present in the 5,300–4,970 y B. maize of San Marcos, we extracted DNA from specimens SM3, SM5, SM9, and SM10 and conducted whole-genome shotgun sequencing.

Whereas SM9 did not yield sufficient endogenous DNA, recovered DNA from SM3, SM5, and SM10 ranged between 775 and 15,334 pg/μL.

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We find that their genetic constitution was similar and influenced by inbreeding, suggesting that the corresponding plants come from a reduced population of isolated and perhaps self-pollinated individuals.