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ece3689-sup-0001-FigS1.docWord document1334KFigure S1. Cluster solutions produced by STRUCTURE and TESS from K = 2 to K = 8. The average membership coefficient of 10 runs from each K is shown. The predefined populations are represented as follows: 1, Oryza sativa (aromatic); 2, O. sativa (japonica); 3, O. sativa (indica); 4, O. sativa (aus); 5, O. nivara from South Asia; 6, O. nivara from Southeast Asia; 7, O. rufipogon from South Asia; 8, O. rufipogon from China; 9, O. rufipogon from continental Southeast Asia; 10, O. rufipogon from insular Southeast Asia; 11, O. rufipogon from Australasia; 12, O. meridionalis from Australasia.
ece3689-sup-0002-FigS2.docWord document1197KFigure S2. Membership coefficients of 10 aligned STRUCTURE runs at K = 4 and K = 6. The predefined populations are represented as follows: 1, Oryza sativa (aromatic); 2, O. sativa (japonica); 3, O. sativa (indica); 4, O. sativa (aus); 5, O. nivara (from South Asia); 6, O. nivara (from Southeast Asia); 7, O. rufipogon (from South Asia); 8, O. rufipogon (from China); 9, O. rufipogon (from continental Southeast Asia); 10, O. rufipogon (from insular Southeast Asia); 11, O. rufipogon (from Australasia); 12, O. meridionalis (from Australasia).
ece3689-sup-0003-FigS3.docWord document6178KFigure S3. (A) Membership coefficients of the 10 aligned TESS runs at K = 2 and K = 3. The predefined populations are represented as follows: 1, South Asian Oryza nivara; 2, Southeast Asian O. nivara; 3, South Asian O. rufipogon; 4, Chinese O. rufipogon; 5, continental Southeast Asian O. rufipogon; 6, insular Southeast Asian O. rufipogon; 7, Australasian O. rufipogon; and 8, O. meridionalis. (B) Membership coefficients of the 10 aligned TESS runs at K = 4 and K = 5. The predefined populations are represented as follows: 1, South Asian O. nivara; 2, Southeast Asian O. nivara; 3, South Asian O. rufipogon; 4, Chinese O. rufipogon; 5, continental Southeast Asian O. rufipogon; 6, insular Southeast Asian O. rufipogon; 7, Australasian O. rufipogon; and 8, O. meridionalis. (C) Membership coefficients of the 10 aligned TESS runs at K = 6 and K = 7. The predefined populations are represented as follows: 1, South Asian O. nivara; 2, Southeast Asian O. nivara; 3, South Asian O. rufipogon; 4, Chinese O. rufipogon; 5, continental Southeast Asian O. rufipogon; 6, insular Southeast Asian O. rufipogon; 7, Australasian O. rufipogon; and 8, O. meridionalis. (D) Membership coefficients of the 10 aligned TESS runs at K = 8 and K = 9. The predefined populations are represented as follows: 1, South Asian O. nivara; 2, Southeast Asian O. nivara; 3, South Asian O. rufipogon; 4, Chinese O. rufipogon; 5, continental Southeast Asian O. rufipogon; 6, insular Southeast Asian O. rufipogon; 7, Australasian O. rufipogon; and 8, O. meridionalis. (E) Membership coefficients of the 10 aligned TESS runs at K = 10. The predefined populations are represented as follows: 1, South Asian O. nivara; 2, Southeast Asian O. nivara; 3, South Asian O. rufipogon; 4, Chinese O. rufipogon; 5, continental Southeast Asian O. rufipogon; 6, insular Southeast Asian O. rufipogon; 7, Australasian O. rufipogon; and 8, O. meridionalis.
ece3689-sup-0004-FigS4.docWord document73KFigure S4. Placement of TESS clusters in the plot of the first two principal coordinate axes (axis 1 on x and axis 2 on y). (A) at K = 4, C1, South Asian Oryza nivara; C2, Southeast Asian O. nivara; C3, continental Asian and insular Southeast Asian O. rufipogon; and C4, O. meridionalis and Australasian O.rufipogon. (B) at K = 7, C1, Indian and Bangladeshi O. nivara; C2, Cambodian O. nivara; C3, continental Asian and insular Southeast Asian O. rufipogon; C4, O. meridionalis; C5, Nepalese O. nivara; C6, non-Cambodian O. nivara; and C7, Australasian O. rufipogon. (C) at K = 8, C1, Indian and Bangladeshi O. nivara; C2, Cambodian O. nivara; C3, Southeast Asian O. rufipogon; C4, O. meridionalis; C5, Nepalese O. nivara; C6, non-Cambodian O. nivara; C7, Australasian O. rufipogon; and C8, South Asian O. rufipogon. Admixed populations are those with less than 0.6 membership coefficient.
ece3689-sup-0005-FigS5.docWord document73KFigure S5. Placement of TESS clusters in the plot of the third and fourth principal coordinate axes (axis 3 on x and axis 4 on y). (A) at K = 4, C1, South Asian Oryza nivara; C2, Southeast Asian O. nivara; C3, continental Asian and insular Southeast Asian O. rufipogon; and C4, O. meridionalis and Australasian O. rufipogon. (B) at K = 7, C1, Indian and Bangladeshi O. nivara; C2, Cambodian O. nivara; C3, continental Asian and insular Southeast Asian O. rufipogon; C4, O. meridionalis; C5, Nepalese O. nivara; C6, Non-Cambodian O. nivara; and C7, Australasian O. rufipogon. (C) at K = 8, C1, Indian and Bangladeshi O. nivara; C2, Cambodian O. nivara; C3, Southeast Asian O. rufipogon; C4, O. meridionalis; C5, Nepalese O. nivara; C6, Non-Cambodian O. nivara; C7, Australasian O. rufipogon; and C8, South Asian O. rufipogon. Admixed populations are those with less than 0.6 membership coefficient.
ece3689-sup-0006-FigS6.docWord document234KFigure S6. Proportion of shared alleles detected in sympatric and nonsympatric population pairs of Oryza meridionalis and O. rufipogon (MR) and of O. nivara and O. rufipogon (NR).
ece3689-sup-0007-TableS1.docWord document338KTable S1. Genetic diversity exhibited by the 125 Oryza series Sativae populations across 29 microsatellite loci.
ece3689-sup-0008-TableS2.docWord document228KTable S2. TESS cluster membership of each population group at K = 8 (averaged over 10 runs).
ece3689-sup-0009-TableS3.docWord document796KTable S3. Allele sizes and frequencies of 29 SSR markers in Asia Pacific Oryza series Sativae. Alleles that can distinguish all or certain population groups within a species are highlighted. Highly discriminating alleles are boldfaced.

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