Table 2.
Compositional Heterogeneity in Mitogenomes
| Conventional Chi-square |
Foster (2004) |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| No rogue |
Protein |
||||||||||
| n missing | 1st | 2nd | 1st RY | 1st RY | 2nd | 1st two-state | 1st RY | 2nd | 1st two-state | ||
| atp6 | 22 | 0.0999 | 1 | 1 | 1 | 1 | 0.2 | 1 | 1 | 0.21 | 1 |
| atp8 | 1 | 1 | 1 | 1 | 1 | 0.36 | 0.53 | 1 | 0.24 | 0.51 | 0.02 |
| cox1–5′ | 142 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0.85 |
| cox1–3′ | 43 | 1 | 1 | 1 | 1 | 1 | 0.95 | 1 | 1 | 0.99 | 1 |
| cox2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| cox3 | 2 | 1 | 1 | 1 | 1 | 1 | 0.82 | 1 | 1 | 0.85 | 0.98 |
| Cytb | 1 | 0.006 | 1 | 1 | 1 | 0.99 | 0.94 | 1 | 0.93 | 0.99 | 0.03 |
| nad1 | 8 | 1 | 1 | 1 | 1 | 1 | 0.34 | 1 | 0.98 | 0.42 | 0.79 |
| nad2 | 148 | 0 | 0.981 | 1 | 1 | 0 | 0 | 0.5 | 0 | 0 | 0 |
| nad3 | 2 | 1 | 1 | 1 | 1 | 0.22 | 0.12 | 1 | 0.14 | 0.22 | 0.45 |
| nad4 | 5 | 0 | 1 | 1 | 1 | 0.01 | 0.01 | 1 | 0 | 0 | 0 |
| nad4L | 5 | 1 | 1 | 1 | 1 | 0.96 | 0.95 | 1 | 0.96 | 0.99 | 0.73 |
| nad5 | 5 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
| nad6 | 5 | 0 | 1 | 1 | 1 | 0 | 0 | 1 | 0.01 | 0 | 0 |
Note.—Each gene was tested for the probability that the data are homogeneous and P values are provided in the table, separately for 1st and 2nd codon positions. Significance of the chi-square statistic was assessed either with the chi-square curve (“conventional chi-square”) or using a null distribution as described in Foster (2004). Note that four loci generally have low probability of homogeneity throughout. n missing, mitogenomes in the matrix not sequenced for a locus; no rogue, analysis conducted with rogue taxa omitted; protein, analysis based on amino acid sequence.