Figure 1.
Light red dots indicate known mexicana populations and larger, dark red dots indicate populations included in the current study.
Figure 2.
Population-level polymorphism and differentiation.
(A) Correlation of percent polymorphic loci in sympatric populations of mexicana and maize. (B) Proportion of shared and privately segregating polymorphisms in mexicana and maize and fixed differences between taxa. Letters above bars indicate sympatric maize/mexicana comparisons (S), maize from a given population versus allopatric mexicana (Ax) and mexicana from a given population versus allopatric maize (Az). (C) Pairwise differentiation (FST) in sympatric and allopatric comparisons of mexicana and maize. (D) Bar plot of assignment proportions from STRUCTURE analysis at K = 2 for mexicana (maroon) and maize (gold) individuals. The Ixtlan maize population was excluded from this figure and the STRUCTURE analysis.
Figure 3.
Detection of introgression across chromosome 4.
(A) Stacked bar plots of the HAPMIX introgression scan across sympatric populations. Population labels are indicated between plots for maize (gold) and mexicana (maroon). Lighter colors indicate introgression initially detected in each population and darker colors show these values after subtracting introgression proportions from jackknife samples of the allopatric reference populations that may be due to false positives. A dotted black line indicates the position of the centromere. (B) Stacked bar plots of the STRUCTURE introgression scan across sympatric populations. The mexicana group is indicated by maroon and the maize group is indicated by gold. The y-axis for each population in (A) and (B) indicates the average admixture proportion across individuals. (C) Genomic regions in maize populations showing greater than 50% membership in mexicana.
Figure 4.
(A) Region of mexicana-to-maize introgression on chromosome 4 (indicated by blue hash on x-axis) shared across seven populations. Above: patterns of introgression seen in San Pedro (blue solid line) and Opopeo (blue dashed line) versus Puruandiro (red solid line) and Ixtlan (red dashed line). Below: pairwise FST of San Pedro/Opopeo (with introgression) versus Puruandiro/Ixtlan (without introgression). (B) Region of mexicana-to-maize introgression on chromosome 9 (indicated by blue hash on x-axis) shared across seven populations. Populations and comparisons are as in Figure 4A. (C) Five leaf sheaths from each of four maize populations grown under highland conditions. (D) Distribution of maize trait values (macrohairs, pigment extent and plant height at 50 days) from growth chamber experiment emulating highland conditions in populations with and without introgression.
Figure 5.
Contribution of mexicana germplasm to a global maize diversity panel.
(A) The difference between the average IBS proportion with mexicana individuals and the average IBS proportion with parviglumis individuals calculated across six groups of modern maize lines identified by Flint-Garcia et al. [81] in the maize association population. Positive values indicate greater IBS with mexicana. (B) Average IBS across chromosome 3 in each line in the maize association population compared to both mexicana and parviglumis. The one-to-one line is indicated by the dashed line. Colors are as in Figure 5A. (C) The proportion of sites across the genome showing greater IBS with mexicana than with parviglumis for each of the six maize association population groups.