Table 1.
Plastid, Mitochondrial, and Nuclear DNA Substitution Rate Statistics from Diverse Plastid-Bearing Lineages
| Lineage | Substitutions Per Site |
dN/dS |
dS Ratio | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Synonymous |
Nonsynonymous |
Functional RNA |
Intergenic |
|||||||||||||
| pt | mt | nuc | pt | mt | nuc | pt | mt | nuc | pt | mt | nuc | pt | mt | nuc | pt:mt:nuc | |
| Archaeplastids | ||||||||||||||||
| Glaucophytes | ||||||||||||||||
| Cyanophora | 1.01 (1.22) | 5.29* (3.17) | 1.21 (0.83) | 0.03 | 0.14 | 0.04 | 0.007 | 0.09 | – | – | – | – | 0.04 | 0.02 | 0.06 | 1:5.3:1.2 |
| Green algae | ||||||||||||||||
| Chlamydomonas | 0.30 (0.11) | 0.29 (0.05) | 0.37 (0.29) | — | 0.01 | 0.02 | — | — | — | 0.67 | 0.38 | — | — | 0.04 | 0.06 | 1:1:1.2 |
| Dunaliella | 0.09 (0.32) | 1.16* (0.52) | — | 0.005 | 0.043 | — | 0.06 | 0.11 | — | — | — | — | 0.09 | 0.04 | — | 1:12.9:— |
| Mesostigma | 0.11 (0.06) | 0.17* (0.11) | 0.27 (0.18) | — | — | — | — | — | — | 0.03 | 0.3 | — | — | — | — | 1:1.5:2.5 |
| Ostreococcus | 0.76 (0.68) | 4.24* (2.48) | 1.68 (2.15) | 0.03 | 0.15 | 0.07 | — | — | — | 0.81 | 1.54 | — | 0.04 | 0.02 | 0.05 | 1:>5:1.9 |
| Land plants | ||||||||||||||||
| Angiosperms | 0.39 (0.01) | 0.13* (0.01) | 2.11 (0.09) | 0.05 | 0.02 | 0.05 | — | — | — | — | — | — | — | — | — | 1:0.3:5.4 |
| Gymnosperms | 0.61 (0.03) | 0.28* (0.02) | 1.23 (0.09) | 0.09 | 0.07 | 0.04 | — | — | — | — | — | — | — | — | — | 1:0.5:2 |
| Red algae | ||||||||||||||||
| Porphyra | 0.47 (0.22) | 1.76* (0.58) | 0.43 (0.18) | 0.03 | 0.09 | 0.01 | 0.01 | 0.06 | 0.04 | 0.17 | 0.25 | 0.15 | 0.06 | 0.05 | 0.04 | 1:3.7:0.9 |
| Haptophytes | ||||||||||||||||
| Emiliania | 0.001 (0.005) | 0.01* (0.008) | — | 0.0001 | 0.0004 | — | 0.0001 | 0.001 | — | 0.0008 | 0.027 | — | — | 0.09 | — | 1:10:— |
| Phaeocystis | 0.25 (0.16) | 2.41* (0.97) | 0.85 (0.54) | 0.01 | 0.09 | 0.05 | 0.005 | 0.18 | 0.006 | — | — | — | 0.06 | 0.05 | 0.07 | 1:9.6:3.4 |
| Stramenopiles | ||||||||||||||||
| Heterosigma | 0.001 (0.003) | 0.012* (0.01) | — | 0.0003 | 0.001 | — | 0 | 0.002 | — | 0.007 | 0.059 | — | 0.21 | 0.11 | — | 1:12:— |
| Nannochloropsis | 0.07 (0.05) | 0.08 (0.04) | — | 0.004 | 0.005 | — | 0.004 | 0.005 | — | — | — | — | 0.11 | 0.07 | — | 1:1.1:— |
Note.—Sources for the data are listed in the Materials and Methods. Abbreviations are as follows: plastid DNA (pt), mitochondrial DNA (mt), and nuclear DNA (nuc); rRNA- and/or tRNA-coding regions (functional RNA); the ratio of nonsynonymous to synonymous substitutions per site (dN/dS); the relative synonymous site substitution rate among plastid, mitochondrial, and nuclear DNAs (dS ratio); data not available (—). Substitution rates at synonymous, nonsynonymous, and intergenic sites as well as dN/dS are based on averages among loci, except for the intergenic substitutions of Emiliania, Heterosigma, and Porphyra, which are based on concatenated data sets. Substitutions at functional RNA-coding sites are all based on concatenated data sets. Asterisk (*) denotes a significance difference (P < 0.05) in the distribution of plastid versus mitochondrial synonymous substitution rates. Bracketed value next to synonymous substitution rate is the standard deviation, expect for angiosperms and gymnosperms where it represents the standard error (Drouin et al. 2008). In some cases, genes showing extreme synonymous site saturation were removed from the analyses (supplementary tables S1–S3, Supplementary Material online).