Table 1. Sequence divergence estimates between SlX9 and SlY9 (K values), and diversity estimates (π values) within SlX9 and in the Silene dioica homologue.
| Region compared (footnotes indicate the sequences that were used) | KS or πS (synonymous or silent sites, see the left-hand column)a | KA or πA (non-synonymous sites) |
|---|---|---|
| SlX9 versus SlY9: raw divergence values | ||
| 392 coding sitesb | 0.153 | 0.00069 |
| 255 nucleotides in exons 2 and 3 (85 codons)c | 0.144 | 0.00026 |
| SlX9 versus SlY9: net divergence (excluding SlX9 polymorphisms)d | ||
| 90 silent sites, SlX9 versus SlY9 | 0.063 | — |
| 255 coding sequence sites (as above) | 0.053 | 0 (small negative value) |
| Long X-linked copies only, versus SlY9, 255 coding sites | 0.042 | 0 |
| Short X-linked copies only, versus SlY9, 255 coding sites | 0.062 | 0 |
| Diversity within S. latifoliae | ||
| X-linked copy, synonymous sites (85 codons in exons 2 and 3) | 0.092 | 0.0005 |
| X-linked copy, 240 silent sites | 0.040 | — |
| Long X-linked copies, 559 silent sites | 0.032 | — |
| Short X-linked copies, 412 silent sites | 0.033 | — |
| Y-linked copy, 283 silent sitesf | 0.0016 | 0 |
| X-linked gene diversity within S. dioica | ||
| 514 silent sitesg | 0.018 | — |
| 117 coding sequence sites | 0.066 | 0.0035 |
a
With Jukes–Cantor correction for saturation.
b
Comparing the longer (Y) sequence from the male parent of the mapping family with the original complementary DNA clone.
c
SlX9 from the diversity study and SlY9 from the male parent of the mapping family.
d
Estimated by subtracting the average of the diversity values.
e
On the basis of single-nucleotide polymorphisms only.
f
It is to be noted that the X and Y estimates of π are based on different gene regions (see Figure 1).
g
From our sample of 18 X-linked sequences; as explained in the text, no Y-linked sequences were amplified from this species.