Table 2.
Estimates of branch length for sister clades of parasitic (P) and autotrophic (non-parasitic, NP) plants for chloroplast sequences
| Comparison | Parasitic clade | Non-parasite |
16S rRNA ( rrn16 ) |
Protein-coding (all) |
Comb. |
dN |
dS |
dN/dS |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P | NP | Sign | P | NP | Sign | Sign | P | NP | Sign | P | NP | Sign | P | NP | Sign | |||
| 1 |
Apodanthaceae |
Malvaceae |
1.637 |
0.013 |
+ |
|
|
|
+ |
|
|
|
|
|
|
|
|
|
| 2 |
Cytinaceae |
Thymelaeaceae |
0.091 |
0.008 |
+ |
|
|
|
+ |
|
|
|
|
|
|
|
|
|
| 3 |
Rafflesiaceae |
Passifloraceae/ Euphorbiaceae |
0.150 |
0.091 |
+ |
|
|
|
+ |
|
|
|
|
|
|
|
|
|
| 4 |
Cynomoriaceae |
Hamamelidacea/ Peridiscaceae |
0.083 |
0.002 |
+ |
|
|
|
+ |
|
|
|
|
|
|
|
|
|
| 5 |
Krameriaceae |
Zygophyllaceae |
|
|
|
0.098 |
0.164 |
– |
– |
0.032 |
0.070 |
– |
0.296 |
0.360 |
– |
0.112 |
0.220 |
– |
| 6 |
Mitrastemonaceae |
Vaccinieae |
0.196 |
0.940 |
– |
|
|
|
– |
|
|
|
|
|
|
|
|
|
| 7 |
Boraginaceae |
Boraginaceae |
|
|
|
0.076 |
0.019 |
+ |
+ |
0.040 |
0.017 |
+ |
0.133 |
0.040 |
+ |
0.297 |
0.423 |
– |
| 8 |
Orobanchaceae |
Plantaginaceae |
0.027 |
0.001 |
+ |
0.561 |
0.366 |
+ |
+ |
0.413 |
0.206 |
+ |
0.960 |
0.743 |
+ |
0.409 |
0.268 |
+ |
| 9 |
Convolvulaceae |
Convolvulaceae/ Ipomoeeae |
0.014 |
0.001 |
+ |
0.724 |
0.052 |
+ |
+ |
0.115 |
0.027 |
+ |
1.938 |
0.151 |
+ |
0.047 |
0.102 |
– |
| 10 |
Lauraceae |
Lauraceae |
|
|
|
0.344 |
0.122 |
+ |
+ |
0.235 |
0.116 |
+ |
0.526 |
0.137 |
+ |
0.320 |
0.721 |
– |
| 11 |
Hydnoraceae |
Aristolochiaceae |
0.336 |
0.000 |
+ |
|
|
|
+ |
|
|
|
|
|
|
|
|
|
| 12 |
Santalaceae/ Olacaceae |
Strombosiaceae |
|
|
|
0.125 |
0.049 |
+ |
+ |
0.068 |
0.039 |
+ |
0.241 |
0.069 |
+ |
0.239 |
0.585 |
– |
|
Wilcoxon rank sign test |
Z = 1.47, p = 0.14 |
Z = 1.68, p = 0.09 |
|
Z = 1.47, p = 0.14 |
Z = 1.89, p = 0.06 |
Z = −1.26, p = 0.21 |
||||||||||||
| Signs test | p = 0.039 | |||||||||||||||||
For details of the species and sequences included in each comparisons see Additional file 3: Table S3. Protein-coding branch lengths were estimated for all substitutions (all), nonsynonymous (dN) and synonymous substitutions (dS): see methods for details. Sign indicates whether the parasite has the longer branch length (+) or not (−). The Wilcoxon ranked signs test takes into account the magnitude of differences in branch length as well as the sign. Because most comparisons had only 16S or the protein-coding genes, we combined the two (Comb.) to assess the pattern over all comparisons using a signs test: for this test we considered only the direction of the rate difference for each comparison, whether calculated from 16S or protein coding genes or both.