Figures and data
Location and appearance of archaeological Bolivian maize (aBM).
a Map of maize sample collection and location information. b Photographs of kernels showing morphological characteristics.
Admixture f3-statistics.
In the form f3 (aBM; Test, tripsacum) where Test represents archaeological and modern samples.
Predicted geographic location of archaeological Bolivian maize (aBM).
The blue point is the predicted locations of aBM based on the SNPs from all archaeological maize. The pink points are the archaeological samples.
Principal Component Analysis (PCA) of nuclear genomic data from archaeological and modern maize.
Samples with greater affinity to one another cluster closer together. Samples with the same color and shape indicate they came from the same country.
Genome-wide distribution of ancient maize specific selective sweeps.
a Signal of selection of modern maize compared to archaeological maize population. Each point indicates a SNP. The blue horizontal line shows the genome-wide significance level (p=1 × 10−6).
Ancient DNA (aDNA) damage pattern of archaeological Bolivian maize (aBM).
a Cytosine deamination damage patterns for the combined bam file of six aBM sequence samples and individual six aBM sequence samples. The position specific substitutions from the 5’ end (red) and the 3’ end (green) of a read. The red line corresponds to C to T substitutions, the green line corresponds to G to A substitutions, and the blue line represents other types of substitutions. b Ancient DNA damage profile. The four upper plots show the base frequencies inside and outside of a read, where the open grey box corresponds to a read. The two lower plots show the position specific substitutions from the 5’ end and the 3’ end of a read. The red line corresponds to C to T substitutions, the blue line corresponds to G to A substitutions, and the fade line represents other types of substitutions.
Archaeological Bolivian maize (aBM) DNA read length.
a Read length distribution of combined aBM bam files prior to hard-masked 5′ thymine and 3′ adenine residues within 5nt of both ends.
Q-Q plot for genome-wide selection in modern maize compared to archaeological maize.
The Q-Q plot between modern and archaeological maize. Each point indicates a value from expected and observed. Red line represents the expected distribution of the p-value, while the blue trend represents the observed distribution.
