Fifteenth century CE Bolivian maize reveals genetic affinities with ancient Peruvian maize
- Genetics and Genome Sciences Program, Michigan State University, United States
- Department of Plant Biology, Michigan State University, United States
- Molecular Plant Sciences Program, Michigan State University, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, United States
- Plant Breeding, Genetics and Biotechnology Program, Michigan State University, United States
- Plant Resilience Institute, Michigan State University, United States
- Genomics Research Centre, Queensland University of Technology, Australia
- Universidad Mayor de San Andres, Bolivia
- Department of Anthropology, Michigan State University, United States
Figures
Figure 1
Location and appearance of archaeological Bolivian maize (aBM).
(a) Map of maize sample collection and location information. (b) Photographs of kernels showing morphological characteristics.
Figure 2
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 gray 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.
Figure 3
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 5 nt of both ends.
Figure 4
Admixture f3-statistics.
In the form f3 (archaeological Bolivian maize, aBM; Test, tripsacum), where Test represents archaeological and modern samples.
Figure 5
Predicted geographic location of archaeological Bolivian maize (aBM).
The blue point is the predicted locations of aBM based on the single-nucleotide polymorphisms (SNPs) from all archaeological maize. The pink points are the archaeological samples.
Figure 6
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.
-
Figure 6—source data 1
Modern sample information.
- https://cdn.elifesciences.org/articles/106818/elife-106818-fig6-data1-v1.pdf
Figure 7
Phylogenetic trees of archaeological Bolivian maize (aBM).
(a) Neighbor-Joining tree with VCF2Pop. (b) Maximum likelihood (ML) tree with SNPhylo. Parv (Zea mays ssp. parviglumis), Zmex (Zea mays ssp. mexicana), Europe (modern Europe), SweetC (model sweet corn), Ztrol (modern Tropical maize), mMexico (modern Mexico), mParaguay (modern Paraguay), mBrazil (modern Brazil), mPeru (modern Peru), mEcuador (modern Ecuador), mGuatemala (modern Guatemala), and mColombia (modern Colombia). Black color is Tripsacum. Red color is the aBM. Red-brown color is modern maize (Zea mays ssp. mays L.). Green color is Teosinte (Zea mays ssp. parviglumis). Blue color is Mexicana teosinte (Zea mays ssp. mexicana).
Figure 8
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.
Figure 9
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 single-nucleotide polymorphism (SNP). The blue horizontal line shows the genome-wide significance level (p=1×10–6).
Additional files
-
Supplementary file 1
(A) Geographical information of the archaeological maize samples used in this study. (B) Paleogenomic characterization of archaeological Bolivian maize sequence samples with six libraries. (C) The percentage of genomic sites covered at variable depths in the archaeological Bolivian maize (aBM) sample 766 (aBMComb_rm5nt.rmDR.bam).
- https://cdn.elifesciences.org/articles/106818/elife-106818-supp1-v1.pdf
-
Source data 1
Known single-nucleotide polymorphisms (SNPs) related to traits.
- https://cdn.elifesciences.org/articles/106818/elife-106818-data1-v1.pdf
-
Source data 2
Single-nucleotide polymorphisms (SNPs) information from SNPVersity.
- https://cdn.elifesciences.org/articles/106818/elife-106818-data2-v1.pdf
-
Source data 3
Gene Ontology (GO) term enrichment information.
- https://cdn.elifesciences.org/articles/106818/elife-106818-data3-v1.pdf
-
MDAR checklist
- https://cdn.elifesciences.org/articles/106818/elife-106818-mdarchecklist1-v1.pdf
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Fifteenth century CE Bolivian maize reveals genetic affinities with ancient Peruvian maize
eLife 14:RP106818.
https://doi.org/10.7554/eLife.106818.3
