Table 1.
Four-Taxon Topology Test.
| Major Topology | Minor Topologies | |
|---|---|---|
| Topologies Testing the Origin Of Domesticated Rice | ||
| ([japonica,O. rufipogon],O. nivara) 5409 (85.1% [84.3–86.0%]) | ([japonica,O. nivara],O. rufipogon) 497 (7.8% [7.2–8.5%]) | ([O. nivara,O. rufipogon],japonica) 446 (7.0% [6.4–7.7%]) |
| ([aus,O. nivara],O. rufipogon) 2214 (65.0% [63.4–66.6%]) | ([aus,O. rufipogon],O. nivara) 975(28.6% [27.1–30.1%]) | ([O. nivara,O. rufipogon],aus) 215 (6.3% [5.5–7.1%]) |
| ([indica,O. nivara],O. rufipogon) 2499 (56.9% [55.5–58.4%]) | ([indica,O. rufipogon],O. nivara) 1447 (33.0% [31.6–34.3%]) | ([O. nivara,O. rufipogon],indica) 444 (10.1% [9.2–11.0%]) |
| Topology Testing the Relationship Between aus and indica | ||
| ([aus,O. nivara],indica) 2854 (58.8% [57.4–60.3%]) | ([aus,indica],O. nivara) 1113 (22.9% [21.7–24.1%]) | ([indica,O. nivara],aus) 883 (18.2% [17.1–19.3%]) |
| Topologies Testing the Relationship Between aus and japonica | ||
| ([japonica,O. rufipogon],aus) 4887 (77.4% [76.4–78.4%]) | ([japonica,aus],O. rufipogon) 972 (15.4% [14.5–16.3%]) | ([aus,O. rufipogon],japonica) 451 (7.1% [6.5–7.8%]) |
| ([aus,O. nivara],japonica) 3062 (67.1% [65.8–68.5%]) | ([japonica,aus],O. nivara) 965 (21.1% [20.0–22.4%]) | ([japonica,O. nivara],aus)535 (11.7% [10.8–12.7%]) |
| Topologies Testing the Relationship Between indica and japonica | ||
| ([japonica,O. rufipogon],indica) 4932 (77.9% [76.9–79.0%]) | ([japonica,indica],O. rufipogon) 947 (15.0% [14.1–15.8%]) | ([indica,O. rufipogon],japonica) 450 (7.1% [6.5–7.8%]) |
| ([indica,O. nivara],japonica) 2562 (59.9% [58.4–61.3%]) | ([japonica,indica],O. nivara) 1025 (23.9% [22.7–25.2%]) | ([japonica,O. nivara],indica) 693 (16.2% [15.1–17.3%]) |
Note.—Total number of gene trees significantly supporting a topology after the Approximately Unbiased (AU) test. Numbers in parenthesis represent percentage with 95% bootstrap confidence interval indicated in square brackets. Oryza punctata was used as outgroup for all topology tests.