The earliest maize from San Marcos cave (Tehuacan, Mexico) is a partial domesticate with genomic evidence of inbreeding

Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacan 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 (Tehuacan, Mexico) yielded non-manipulated and intact maize specimens dating at a similar age of 5300 to 4970 calibrated years before present (BP). On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, here we show that the earliest maize from San Marcos cave was a partial domesticate diverging from the landrace monophyletic lineage and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci such as teosinte branched1 (tb1) and brittle endosperm2 (br2) 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 diversity that are absent from extant maize. Genetic comparisons among three temporally convergent samples revealed that they were highly homozygous and identical by descent across their genome. Our results indicate that the earliest maize from San Marcos cave was strongly inbred, opening the possibility for Tehuacan maize cultivation evolving from small and isolated self-pollinated populations that suffered from reduced biological fitness.