Table 3. Pairwise comparisons of trees inferred from plastome partitions differing by the inclusion or exclusion of positively selected sites and gapped sites.
| Positively selected sites included or excluded | Gapped sites included or excluded | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A vs. C | B vs. D | E vs. G | F vs. H | W vs. Y | X vs. Z | A vs. B | C vs. D | E vs. F | G vs. H | Q vs. R | W vs. X | Y vs. Z | |||
| Number of shared clades with BP ≥50% | 201 | 192 | 227 | 229 | 233 | 238 | 220 ± 17 | 200 | 197 | 230 | 228 | 211 | 227 | 224 | 215 ± 14 |
| Number (%) of shared clades with BP = 100% | 106 (53) | 90 (47) | 185 (81) | 185 (81) | 203 (87) | 198 (83) | 160 ± 45 | 104 (52) | 95 (48) | 184 (80) | 185 (81) | 158 (75) | 200 (88) | 189 (84) | 159 ± 40 |
| Number of clades with BP ≥50% (≥70%) in one tree and <50% in the other | 13(4) in A, 14(2) in C | 19(5) in B, 14(6) in D | 12(4) in E, 10(3) in G | 9(5) in F, 8 (2) in H | 11(10) in W, 15(11) in Y | 4(0) in X, 2(1) in Z | 14(7) in A, 11(3) in B | 18(7) in C, 9(2) in D | 9(1) in E, 8(4) in F | 10(3) in G, 8(2) in H | 31(20) in Q, 14(9) in R | 11(3) in W, 15(8) in X | 22(16) in Y, 22(11) in Z | ||
| Range of support difference | −39 to 41 | −29 to 40 | −27 to 26 | −30 to 22 | −20 to 30 | −48 to 40 | −16 to 33 | −44 to 33 | −28 to 18 | −27 to 30 | −30 to 43 | −22 to 31 | −23 to 40 | ||
| Mean support difference ± s.d. [absolute mean support difference ± s.d.] | 2 ± 9 [4 ± 9] | 1 ± 9 [4 ± 8] | 1 ± 5 [2 ± 5] | 0 ± 4 [1 ± 4] | 0 ± 4 [1 ± 4] | 0 ± 7 [2 ± 7] | 2 ± 5 [3 ± 5] | 0 ± 9 [4 ± 8] | 0 ± 4 [2 ± 4] | 0 ± 5 [2 ± 5] | 3 ± 8 [3 ± 8] | 1 ± 5 [1 ± 5] | 1 ± 6 [2 ± 6] | ||
| Number of shared clades with identical support | 114 | 100 | 188 | 189 | 205 | 201 | 166 ± 42 | 112 | 103 | 187 | 191 | 159 | 201 | 193 | 164 ± 38 |
| Number of shared clades with increased support when positively selected/gapped sites removed | 29 | 46 | 15 | 16 | 16 | 11 | 22 ± 12 | 20 | 32 | 15 | 19 | 3 | 5 | 9 | 15 ± 9 |
| Number of shared clades with decreased support when positively selected/gapped sites removed | 58 | 46 | 24 | 24 | 12 | 26 | 32 ± 15 | 68 | 62 | 28 | 19 | 49 | 21 | 22 | 38 ± 13 |
Note:
For each comparison the table records the number of shared (identical) clades with bootstrap support (BP) ≥50%, maximum BP, identical BP, and BP ≥50% and ≥70% in one tree but <50% in the other; the range of BP difference and mean difference in BP for shared clades when positively selected and gapped sites are excluded; and the numbers of shared clades for which BP increases and decreases when positively selected and gapped sites are excluded.